Methods of predicting distant metastasis of lymph node-negative primary breast cancer using biological pathway gene expression analysis

ABSTRACT

The present invention provides a method for predicting distant metastasis of lymph node negative primary breast cancer by obtaining breast cancer cells; isolating nucleic acid and/or protein from the cells; and analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker selected from the pathways in Table 2.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

No government funds were used to make this invention.

REFERENCE TO SEQUENCE LISTING, OR A COMPUTER PROGRAM LISTING COMPACT DISK APPENDIX

Reference to a “Sequence Listing”, a table, or a computer program listing appendix submitted on a compact disc and an incorporation by reference of the material on the compact disc including duplicates and the files on each compact disc shall be specified.

BACKGROUND OF THE INVENTION

Microarray technology has become a popular tool to classify breast cancer patients into subtypes, relapse and non-relapse, type of relapse, responder and non-responder³⁻¹¹. A concern for application of gene expression profiling is stability of the gene list as a signature¹². Considering that many genes have correlated expression on a chip, especially for genes involved in the same biological process, it is quite possible that different genes may be present in different signatures when different training sets of patients are used. Gene signatures to date for separating patients into different risk groups were derived based on the performance of individual genes, regardless of its biological processes or functions. It has been suggested that it might be more appropriate to interrogate the gene list for biological themes, rather than for individual genes^(1,2,8,13-19).

SUMMARY OF THE INVENTION

The present invention provides a method for predicting distant metastasis of lymph node negative primary breast cancer by obtaining breast cancer cells; isolating nucleic acid and/or protein from the cells; and analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker selected from the pathways in Table 2.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 Evaluation of the 500 gene signatures. Each of the 100-gene signatures for 80 randomly selected tumors in the training set was used to predict relapsed patients in the corresponding test set. Its performance was measured by the AUC of the ROC analysis. (a) Performance of the gene signatures for ER-positive patients in test sets. (b) Performance of the gene signatures for ER-negative patients in test sets. Distribution of AUC for the 500 prognostic signatures (left panels) as derived following the flow chart presented in FIG. 4. Distribution of AUC for the 500 random gene lists (right panels). To generate a gene list as a control, the clinic information for the ER-positive patients or ER-negative patients was permutated randomly and reassigned to the chip data.

FIG. 2 Association of the expression of individual genes with DMFS time for selected over-represented pathways. Geneplot function in the Global Test program^(1,2) was applied and the contribution of the individual genes in each selected pathway was plotted. The numbers at the X-axis represent the number of genes in the respective pathway in ER-positive or ER-negative tumors. The values at the Y-axis, represent the contribution (influence) of each individual gene in the selected pathway with DMFS. Negative values indicate there is no association between the gene expression and DMFS. Each thin horizontal line in a bar (influence) indicates one standard deviation away from the reference point, two or more horizontal lines in a bar indicates that the association of the corresponding gene with DMFS is statistically significant. The green bars reflect genes that are positively associated with DMFS, indicating a higher expression in tumors without metastatic capability. The red bars reflect genes that are negatively associated with DMFS, indicative of higher expression in tumors with metastatic capability. (a) Apoptosis pathway consisting of 282 genes in ER-positive tumors. (b) Regulation of cell growth pathway consisting of 58 genes in ER-negative tumors. (c) Regulation of cell cycle pathway consisting of 228 genes in ER-positive tumors. (d) Cell adhesion pathway consisting of 327 genes in ER-negative tumors. (e) Immune response pathway consisting of 379 genes in ER-positive tumors. (f) Regulation of G-coupled receptor signaling pathway consisting of 20 genes in ER-negative tumors. (g) Mitosis pathway consisting of 100 genes in ER-positive tumors. (h) Skeletal development pathway consisting of 105 genes in ER-negative tumors.

FIG. 3 Validation of pathway-based breast cancer classifiers constructed from the optimal significant genes of the two most significant pathways for both ER-positive and ER-negative tumors. A recently published data set for which samples were hybridized on Affymetrix U133A chip²¹, including 189 invasive breast carcinomas with survival information, was used. Among them, 153 tumors were from lymph node negative patients. After removing one patient who died 15 days after surgery, the remaining 152 patients were used to validate the signatures. The 152 patients set consisted of 125 ER-positive tumors and 27 ER-negative tumors based on the expression level of ER gene on the chip. (a) Receiver operating characteristic (ROC) analysis of the 38-gene signature for ER-positive tumors. (b) Kaplan-Meier analysis of patients with ER-positive tumors as a function of the 38-gene signature. The DMFS probabilities (and their 95% confidence intervals) at 60 and 120 months, respectively, were 92.7% (86.0% to 99.9%), or 74.5% (62.0% to 89.5%) for the good signature curve, 59.9%% (49.0% to 73.2%), or 48.5% (36.8% to 63.9%) for the poor signature curve. (c) ROC analysis of the 12-gene signature for ER-negative tumors. (d) Kaplan-Meier analysis of patients with ER-negative tumors as function of the 12-gene signature. The DMFS probabilities (and their 95% confidence intervals) at 60 and 120 months, respectively, were both 94.1% (83.6% to 100%) for the good signature curve, and 40.0% (18.7% to 85.5%), or 26.7% (8.9% to 80.3%) for the poor signature curve. (e) ROC analysis of a combined 50-gene signatures for ER-positive and ER-negative tumors. (f) Kaplan-Meier analysis of 152 breast cancer patients as a function of the 50-gene signature. The DMFS probabilities (and their 95% confidence intervals) at 60 and 120 months, respectively, were 93.0% (87.3% to 99.1%), or 79.3% (69.2% to 91.0%) for the good signature curve, and 57.2% (46.9% to 69.7%), or 45.4% (34.6% to 59.7%) for the poor signature curve.

FIG. 4 shows a work flow of data analysis.

FIG. 5 shows top 20 prognostic pathways in ER-positive tumors obtained from Association of the expression of individual genes with DMFS time for selected over-represented pathways. Geneplot function in the Global Test program^(1,2) was applied and the contribution of the individual genes in each selected pathway is plotted. The numbers at the X-axis represent the number of genes in the respective pathway in ER-positive tumors. The values at the Y-axis, represent the contribution (influence) of each individual gene in the selected pathway with DMFS. Negative values indicate there is no association between the gene expression and DMFS. Each thin horizontal line in a bar (influence) indicates one standard deviation away from the reference point, two or more horizontal lines in a bar indicates that the association of the corresponding gene with DMFS is statistically significant. The green bars reflect genes that are positively associated with DMFS, indicating a higher expression in tumors without metastatic capability. The red bars reflect genes that are negatively associated with DMFS, indicative of higher expression in tumors with metastatic capability.

DETAILED DESCRIPTION

The present invention provides a method for predicting distant metastasis of lymph node negative primary breast cancer by obtaining breast cancer cells; isolating nucleic acid and/or protein from the cells; and analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker selected from the pathways in Table 2.

A Biomarker is any indicia of an indicated Marker nucleic acid/protein. Nucleic acids can be any known in the art including, without limitation, nuclear, mitochondrial (homeoplasmy, heteroplasmy), viral, bacterial, fungal, mycoplasmal, etc. The indicia can be direct or indirect and measure over- or under-expression of the gene given the physiologic parameters and in comparison to an internal control, placebo, normal tissue or another carcinoma. Biomarkers include, without limitation, nucleic acids and proteins (both over and under-expression and direct and indirect). Using nucleic acids as Biomarkers can include any method known in the art including, without limitation, measuring DNA amplification, deletion, insertion, duplication, RNA, micro RNA (miRNA), loss of heterozygosity (LOH), single nucleotide polymorphisms (SNPs, Brookes (1999)), copy number polymorphisms (CNPs) either directly or upon genome amplification, microsatellite DNA, epigenetic changes such as DNA hypo- or hyper-methylation and FISH. Using proteins as Biomarkers includes any method known in the art including, without limitation, measuring amount, activity, modifications such as glycosylation, phosphorylation, ADP-ribosylation, ubiquitination, etc., or immunohistochemistry (IHC) and turnover. Other Biomarkers include imaging, molecular profiling, cell count and apoptosis Markers.

“Origin” as referred to in ‘tissue of origin’ means either the tissue type (lung, colon, etc.) or the histological type (adenocarcinoma, squamous cell carcinoma, etc.) depending on the particular medical circumstances and will be understood by anyone of skill in the art.

A Marker gene corresponds to the sequence designated by a SEQ ID NO when it contains that sequence. A gene segment or fragment corresponds to the sequence of such gene when it contains a portion of the referenced sequence or its complement sufficient to distinguish it as being the sequence of the gene. A gene expression product corresponds to such sequence when its RNA, mRNA, or cDNA hybridizes to the composition having such sequence (e.g. a probe) or, in the case of a peptide or protein, it is encoded by such mRNA. A segment or fragment of a gene expression product corresponds to the sequence of such gene or gene expression product when it contains a portion of the referenced gene expression product or its complement sufficient to distinguish it as being the sequence of the gene or gene expression product.

The inventive methods, compositions, articles, and kits of described and claimed in this specification include one or more Marker genes. “Marker” or “Marker gene” is used throughout this specification to refer to genes and gene expression products that correspond with any gene the over- or under-expression of which is associated with an indication or tissue type.

Preferred methods for establishing gene expression profiles include determining the amount of RNA that is produced by a gene that can code for a protein or peptide. This is accomplished by reverse transcriptase PCR (RT-PCR), competitive RT-PCR, real time RT-PCR, differential display RT-PCR, Northern Blot analysis and other related tests. While it is possible to conduct these techniques using individual PCR reactions, it is best to amplify complementary DNA (cDNA) or complementary RNA (cRNA) produced from mRNA and analyze it via microarray. A number of different array configurations and methods for their production are known to those of skill in the art and are described in for instance, U.S. Pat. Nos. 5,445,934; 5,532,128; 5,556,752; 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,561,071; 5,571,639; 5,593,839; 5,599,695; 5,624,711; 5,658,734; and 5,700,637.

Microarray technology allows for the measurement of the steady-state mRNA level of thousands of genes simultaneously thereby presenting a powerful tool for identifying effects such as the onset, arrest, or modulation of uncontrolled cell proliferation. Two microarray technologies are currently in wide use. The first are cDNA arrays and the second are oligonucleotide arrays. Although differences exist in the construction of these chips, essentially all downstream data analysis and output are the same. The product of these analyses are typically measurements of the intensity of the signal received from a labeled probe used to detect a cDNA sequence from the sample that hybridizes to a nucleic acid sequence at a known location on the microarray. Typically, the intensity of the signal is proportional to the quantity of cDNA, and thus mRNA, expressed in the sample cells. A large number of such techniques are available and useful. Preferred methods for determining gene expression can be found in U.S. Pat. Nos. 6,271,002; 6,218,122; 6,218,114; and 6,004,755.

Analysis of the expression levels is conducted by comparing such signal intensities. This is best done by generating a ratio matrix of the expression intensities of genes in a test sample versus those in a control sample. For instance, the gene expression intensities from a diseased tissue can be compared with the expression intensities generated from benign or normal tissue of the same type. A ratio of these expression intensities indicates the fold-change in gene expression between the test and control samples.

The selection can be based on statistical tests that produce ranked lists related to the evidence of significance for each gene's differential expression between factors related to the tumor's original site of origin. Examples of such tests include ANOVA and Kruskal-Wallis. The rankings can be used as weightings in a model designed to interpret the summation of such weights, up to a cutoff, as the preponderance of evidence in favor of one class over another. Previous evidence as described in the literature may also be used to adjust the weightings.

A preferred embodiment is to normalize each measurement by identifying a stable control set and scaling this set to zero variance across all samples. This control set is defined as any single endogenous transcript or set of endogenous transcripts affected by systematic error in the assay, and not known to change independently of this error. All Markers are adjusted by the sample specific factor that generates zero variance for any descriptive statistic of the control set, such as mean or median, or for a direct measurement. Alternatively, if the premise of variation of controls related only to systematic error is not true, yet the resulting classification error is less when normalization is performed, the control set will still be used as stated. Non-endogenous spike controls could also be helpful, but are not preferred.

Gene expression profiles can be displayed in a number of ways. The most common is to arrange raw fluorescence intensities or ratio matrix into a graphical dendogram where columns indicate test samples and rows indicate genes. The data are arranged so genes that have similar expression profiles are proximal to each other. The expression ratio for each gene is visualized as a color. For example, a ratio less than one (down-regulation) appears in the blue portion of the spectrum while a ratio greater than one (up-regulation) appears in the red portion of the spectrum. Commercially available computer software programs are available to display such data including “Genespring” (Silicon Genetics, Inc.) and “Discovery” and “Infer” (Partek, Inc.)

In the case of measuring protein levels to determine gene expression, any method known in the art is suitable provided it results in adequate specificity and sensitivity. For example, protein levels can be measured by binding to an antibody or antibody fragment specific for the protein and measuring the amount of antibody-bound protein. Antibodies can be labeled by radioactive, fluorescent or other detectable reagents to facilitate detection. Methods of detection include, without limitation, enzyme-linked immunosorbent assay (ELISA) and immunoblot techniques.

Modulated genes used in the methods of the invention are described in the Examples. The genes that are differentially expressed are either up regulated or down regulated in patients with carcinoma of a particular origin relative to those with carcinomas from different origins. Up regulation and down regulation are relative terms meaning that a detectable difference (beyond the contribution of noise in the system used to measure it) is found in the amount of expression of the genes relative to some baseline. In this case, the baseline is determined based on the algorithm. The genes of interest in the diseased cells are then either up regulated or down regulated relative to the baseline level using the same measurement method. Diseased, in this context, refers to an alteration of the state of a body that interrupts or disturbs, or has the potential to disturb, proper performance of bodily functions as occurs with the uncontrolled proliferation of cells. Someone is diagnosed with a disease when some aspect of that person's genotype or phenotype is consistent with the presence of the disease. However, the act of conducting a diagnosis or prognosis may include the determination of disease/status issues such as determining the likelihood of relapse, type of therapy and therapy monitoring. In therapy monitoring, clinical judgments are made regarding the effect of a given course of therapy by comparing the expression of genes over time to determine whether the gene expression profiles have changed or are changing to patterns more consistent with normal tissue.

Genes can be grouped so that information obtained about the set of genes in the group provides a sound basis for making a clinically relevant judgment such as a diagnosis, prognosis, or treatment choice. These sets of genes make up the portfolios of the invention. As with most diagnostic Markers, it is often desirable to use the fewest number of Markers sufficient to make a correct medical judgment. This prevents a delay in treatment pending further analysis as well unproductive use of time and resources.

One method of establishing gene expression portfolios is through the use of optimization algorithms such as the mean variance algorithm widely used in establishing stock portfolios. This method is described in detail in 20030194734. Essentially, the method calls for the establishment of a set of inputs (stocks in financial applications, expression as measured by intensity here) that will optimize the return (e.g., signal that is generated) one receives for using it while minimizing the variability of the return. Many commercial software programs are available to conduct such operations. “Wagner Associates Mean-Variance Optimization Application,” referred to as “Wagner Software” throughout this specification, is preferred. This software uses functions from the “Wagner Associates Mean-Variance Optimization Library” to determine an efficient frontier and optimal portfolios in the Markowitz sense is preferred. Markowitz (1952). Use of this type of software requires that microarray data be transformed so that it can be treated as an input in the way stock return and risk measurements are used when the software is used for its intended financial analysis purposes.

The process of selecting a portfolio can also include the application of heuristic rules. Preferably, such rules are formulated based on biology and an understanding of the technology used to produce clinical results. More preferably, they are applied to output from the optimization method. For example, the mean variance method of portfolio selection can be applied to microarray data for a number of genes differentially expressed in subjects with cancer. Output from the method would be an optimized set of genes that could include some genes that are expressed in peripheral blood as well as in diseased tissue. If samples used in the testing method are obtained from peripheral blood and certain genes differentially expressed in instances of cancer could also be differentially expressed in peripheral blood, then a heuristic rule can be applied in which a portfolio is selected from the efficient frontier excluding those that are differentially expressed in peripheral blood. Of course, the rule can be applied prior to the formation of the efficient frontier by, for example, applying the rule during data pre-selection.

Other heuristic rules can be applied that are not necessarily related to the biology in question. For example, one can apply a rule that only a prescribed percentage of the portfolio can be represented by a particular gene or group of genes. Commercially available software such as the Wagner Software readily accommodates these types of heuristics. This can be useful, for example, when factors other than accuracy and precision (e.g., anticipated licensing fees) have an impact on the desirability of including one or more genes.

The gene expression profiles of this invention can also be used in conjunction with other non-genetic diagnostic methods useful in cancer diagnosis, prognosis, or treatment monitoring. For example, in some circumstances it is beneficial to combine the diagnostic power of the gene expression based methods described above with data from conventional Markers such as serum protein Markers (e.g., Cancer Antigen 27.29 (“CA 27.29”)). A range of such Markers exists including such analytes as CA 27.29. In one such method, blood is periodically taken from a treated patient and then subjected to an enzyme immunoassay for one of the serum Markers described above. When the concentration of the Marker suggests the return of tumors or failure of therapy, a sample source amenable to gene expression analysis is taken. Where a suspicious mass exists, a fine needle aspirate (FNA) is taken and gene expression profiles of cells taken from the mass are then analyzed as described above. Alternatively, tissue samples may be taken from areas adjacent to the tissue from which a tumor was previously removed. This approach can be particularly useful when other testing produces ambiguous results.

The present invention provides a method for analyzing a biological specimen for the presence of cells specific for an indication by: a) enriching cells from the specimen; b) isolating nucleic acid and/or protein from the cells; and c) analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker specific for the indication.

The biological specimen can be any known in the art including, without limitation, urine, blood, serum, plasma, lymph, sputum, semen, saliva, tears, pleural fluid, pulmonary fluid, bronchial lavage, synovial fluid, peritoneal fluid, ascites, amniotic fluid, bone marrow, bone marrow aspirate, cerebrospinal fluid, tissue lysate or homogenate or a cell pellet. See, e.g. 20030219842.

The indication can include any known in the art including, without limitation, cancer, risk assessment of inherited genetic pre-disposition, identification of tissue of origin of a cancer cell such as a CTC 60/887,625, identifying mutations in hereditary diseases, disease status (staging), prognosis, diagnosis, monitoring, response to treatment, choice of treatment (pharmacologic), infection (viral, bacterial, mycoplasmal, fungal), chemosensitivity U.S. Pat. No. 7,112,415, drug sensitivity, metastatic potential or identifying mutations in hereditary diseases.

Cells enrichment can be by any method known in the art including, without limitation, by antibody/magnetic separation, (Immunicon, Miltenyi, Dynal) U.S. Pat. No. 6,602,422, 5,200,048, fluorescence activated cell sorting, (FACs) U.S. Pat. No. 7,018,804, filtration or manually. The manual enrichment can be for instance by prostate massage. Goessl et al. (2001) Urol 58:335-338.

The nucleic acid can be any known in the art including, without limitation, is nuclear, mitochondrial (homeoplasmy, heteroplasmy), viral, bacterial, fungal or mycoplasmal.

Methods of isolating nucleic acid and protein are well known in the art. See e.g. U.S. Pat. No. 6,992,182, RNA www.aibion.com/techlib/basics/rnaisol/index.htlm, and 20070054287.

DNA analysis can be any known in the art including, without limitation, methylation, de-methylation, karyotyping, ploidy (aneuploidy, polyploidy), DNA integrity (assessed through gels or spectrophotometry), translocations, mutations, gene fusions, activation—de-activation, single nucleotide polymorphisms (SNPs), copy number or whole genome amplification to detect genetic makeup. RNA analysis includes any known in the art including, without limitation, q-RT-PCR, miRNA or post-transcription modifications. Protein analysis includes any known in the art including, without limitation, antibody detection, post-translation modifications or turnover. The proteins can be cell surface markers, preferably epithelial, endothelial, viral or cell type. The Biomarker can be related to viral/bacterial infection, insult or antigen expression.

The claimed invention can be used for instance to determine metastatic potential of a cell from a biological specimen by isolating nucleic acid and/or protein from the cells; and analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker specific for metastatic potential.

The cells of the claimed invention can be used for instance to identify mutations in hereditary diseases cell from a biological specimen by isolating nucleic acid and/or protein from the cells; and analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker specific for specific for a hereditary disease.

The cells of the claimed invention can be used for instance to obtain and preserve cellular material and constituent parts thereof such as nucleic acid and/or protein. The constituent parts can be used for instance to make tumor cell vaccines or in immune cell therapy. 20060093612, 20050249711.

Kits made according to the invention include formatted assays for determining the gene expression profiles. These can include all or some of the materials needed to conduct the assays such as reagents and instructions and a medium through which Biomarkers are assayed.

Articles of this invention include representations of the gene expression profiles useful for treating, diagnosing, prognosticating, and otherwise assessing diseases. These profile representations are reduced to a medium that can be automatically read by a machine such as computer readable media (magnetic, optical, and the like). The articles can also include instructions for assessing the gene expression profiles in such media. For example, the articles may comprise a CD ROM having computer instructions for comparing gene expression profiles of the portfolios of genes described above. The articles may also have gene expression profiles digitally recorded therein so that they may be compared with gene expression data from patient samples. Alternatively, the profiles can be recorded in different representational format. A graphical recordation is one such format. Clustering algorithms such as those incorporated in “DISCOVERY” and “INFER” software from Partek, Inc. mentioned above can best assist in the visualization of such data.

Different types of articles of manufacture according to the invention are media or formatted assays used to reveal gene expression profiles. These can comprise, for example, microarrays in which sequence complements or probes are affixed to a matrix to which the sequences indicative of the genes of interest combine creating a readable determinant of their presence. Alternatively, articles according to the invention can be fashioned into reagent kits for conducting hybridization, amplification, and signal generation indicative of the level of expression of the genes of interest for detecting cancer.

The present invention defines specific marker portfolios that have been characterized to detect a single circulating breast tumor cell in a background of peripheral blood. The molecular characterization multiplex assay portfolio has been optimized for use as a QRT-PCR multiplex assay where the molecular characterization multiplex contains 2 tissue of origin markers, 1 epithelial marker and a housekeeping marker. QRT-PCR will be carried out on the Smartcycler II for the molecular characterization multiplex assay. The molecular characterization singlex assay portfolio has been optimized for use as a QRT-PCR assay where each marker is run in a single reaction that utilizes 3 cancer status markers, 1 epithelial marker and a housekeeping marker. Unlike the RPA multiplex assay the molecular characterization singlex assay will be run on the Applied Biosystems (ABI) 7900HT and will use a 384 well plate as it platform. The molecular characterization multiplex assay and singlex assay portfolios accurately detect a single circulating epithelial cell enabling the clinician to predict recurrence. The molecular characterization multiplex assay utilizes Thermus thermophilus (TTH) DNA polymerase due to its ability to carry out both reverse transcriptase and polymerase chain reaction in a single reaction. In contrast, the molecular characterization singlex assay utilizes the Applied Biosystems One-Step Master Mix which is a two enzyme reaction incorporating MMLV for reverse transcription and Taq polymerase for PCR. Assay designs are specific to RNA by the incorporation of an exon-intron junction so that genomic DNA is not efficiently amplified and detected.

Knowledge of biological processes may be more relevant for understanding of the disease than information on differentially expressed genes. We have investigated distinct biological pathways associated with the metastatic capability of lymph-node negative primary breast tumors. A re-sampling method was used to create 500 different training sets, and to derive the corresponding gene signatures for estrogen receptor (ER)-positive and -negative tumors. The constructed gene signatures were mapped to Gene Ontology Biological Process (GOBP) to identify over-represented pathways related to patient outcomes. Global Test program^(1,2) was used to confirm that these biological pathways were associated with the development of metastases. Furthermore, by mapping 4 published prognostic gene signatures with more than 60 genes to the top 20 pathways, each of them can be mapped to 19 of the top distinct pathways despite a minimum overlap of identical genes. Our study provides a new way to understand the mechanisms of breast cancer progression and to derive a pathway-based signatures for prognosis.

We investigated the various prognostic gene signatures derived from different patient groups with an aim towards understanding the underlying biological pathways. Since gene expression patterns of ER-subgroups of breast tumors are quite different^(3-6,8,20), data analysis to derive gene signatures and subsequent pathway analysis was conducted separately⁸. For either ER-positive or ER-negative patients, 80 samples were randomly selected as a training set and the top 100 genes were used as a signature to predict tumor recurrence for the remaining ER-positive or ER-negative patients (FIG. 4). The area under curve (AUC) of receiver operating characteristic (ROC) analysis with distant metastasis within 5 years as a defining point was used as a measurement of the performance of a signature in a corresponding test set. The above procedure was repeated 500 times. The average of AUCs for the 500 signatures in the test sets was 0.70 whereas the average of AUCs for the 500 control gene lists was 0.50, indicating random prediction (FIG. 1 a). For ER-negative datasets, these values were 0.67 and 0.51, respectively (FIG. 1 b). Multiple gene signatures could be identified with similar performance while the genes in individual signatures can be substituted. The top 20 genes ranked by their frequency in the 500 signatures for ER-positive or ER-negative tumors are shown in Table 1. The most frequently present genes were those for KIAA0241 protein (KIAA0241) for ER-positive tumors, and zinc finger protein multitype 2 (ZFPM2) for ER-negative tumors, respectively, while there was no overlap between genes of the two core gene lists. For Sequence ID Numbers see the sequence listing table.

TABLE 1 Genes with highest frequencies in 500 signatures Gene title Gene symbol Frequency Top 20 core genes from ER-positive tumors KIAA0241 protein KIAA0241 321 CD44 antigen (homing function and Indian blood group system) CD44 286 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 ABCC5 251 serine/threonine kinase 6 STK6 245 cytochrome c, somatic CYCS 235 KIAA0406 gene product KIA0406 212 uridine-cytidine kinase 1-like 1 UCKL1 201 zinc finger, CCHC domain containing 8 ZCCHC8 188 Rac GTPase activating protein 1 RACGAP1 186 staufen, RNA binding protein (Drosophila) STAU 176 lactamase, beta 2 LACTB2 175 eukaryotic translation elongation factor 1 alpha 2 EEF1A2 172 RAE1 RNA export 1 homolog (S. pombe) RAE1 153 tuftelin 1 TUFT1 150 zinc finger protein 36, C3H type-like 2 ZFP36L2 150 origin recognition complex, subunit 6 homolog-like (yeast) ORC6L 143 zinc finger protein 623 ZNF623 140 extra spindle poles like 1 ESPL1 139 transcription elongation factor B (SIII), polypeptide 1 TCEB1 138 ribosomal protein S6 kinase, 70 kDa, polypeptide 1 RPS6KB1 127 Top 20 core genes from ER-negative tumors zinc finger protein, multitype 2 ZFPM2 445 ribosomal protein L26-like 1 RPL26L1 372 hypothetical protein FLJ14346 FLJ14346 372 mitogen-activated protein kinase-activated protein kinase 2 MAPKAPK2 347 collagen, type II, alpha 1 COL2A1 340 muscleblind-like 2 (Drosophila) MBNL2 320 G protein-coupled receptor 124 GPR124 314 splicing factor, arginine/serine-rich 11 SFRS11 300 heterogeneous nuclear ribonucleoprotein A1 HNRPA1 297 CDC42 binding protein kinase alpha (DMPK-like) CDC42BPA 296 regulator of G-protein signalling 4 RGS4 276 transient receptor potential cation channel, subfamily C, member 1 TRPC1 265 transcription factor 8 (represses interleukin 2 expression) TCF8 263 chromosome 6 open reading frame 210 C6orf210 262 dynamin 3 DNM3 260 centrosome protein Cep63 Cep63 251 tumor necrosis factor (ligand) superfamily, member 13 TNFSF13 251 dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis) DACT1 248 heterogeneous nuclear ribonucleoprotein A1 HNRPA1 245 reversion-inducing-cysteine-rich protein with kazal motifs RECK 243

In Table 1, the top 20 genes are ranked by their frequency in the 500 signatures of 100 genes for ER-positive and ER-negative tumors (for details see FIG. 4).

The biological pathways are distinct for ER-positive and -negative tumors. For ER-positive tumors, many pathways that are related with cell division are present in the top 20 over-represented pathways, in addition to a couple of immune-related pathways (Table 4).

TABLE 4 Top 20 pathways over-represented in the 500 signatures and evaluation by Global Test program Pathways for ER+ tumors Pathways for ER− tumors GO_Process GO_ID Frequency GO_Process GO_ID Frequency mitosis 7067 256 nuclear mRNA splicing, via spliceosome 398 203 apoptosis 6915 250 RNA splicing 8380 192 oncogenesis 7084 228 protein complex assembly 6461 183 regulation of cell cycle 74 203 endocytosis 6897 166 cell surface recepter-linked signal 7166 172 skeletal development 1501 160 transduction immune response 6955 167 cation transport 6812 160 cytokinesis 910 165 signal transduction 7165 160 ubiquitin-dependent protein catabolism 6511 158 regulation of G-protein coupled receptor signaling 8277 153 DNA repair 6281 156 protein amino acid phosphorylation 6468 151 protein biosynthesis 6412 145 regulation of cell growth 1558 136 intracellular protein transport 6886 141 intracellular signaling cascade 7242 135 cell cycle 7049 138 protein modification 6464 132 cellular defense response 6968 131 cell adhesion 7155 110 induction of apoptosis 6917 115 regulation of transcription from Pol II promoter 6357 109 protein amino acid phosphorylation 6468 114 protein biosynthesis 6412 99 mitotic chromosome segregation 70 98 calcium ion transport 6816 93 cell motility 6928 93 regulation of cell cycle 74 88 DNA replication 6260 92 carbohydrate metabolism 5975 86 chemotaxis 6935 89 mRNA processing 6397 81 metabolism 8152 83 cell cycle 7049 72

All of the 20 pathways had a significant association with distant metastasis-free survival (DMFS) by Global Testing program. The top 2 most significant being Apoptosis, and Regulation of cell cycle (Table 2). For ER-negative tumors, many of the top 20 pathways are related with RNA processing, transportation and signal transduction (Table 4). Eighteen of the top 20 pathways demonstrated significant association with DMFS, the 2 most significant being Regulation of cell growth, and Regulation of G-protein coupled receptor signaling (Table 2).

TABLE 2 Top 20 pathways in the 500 signatures of ER-positive and ER-negative tumors evaluated by Global Test Pathways GO_ID P Frequency ER-positive tumors Apoptosis 6915 3.06E−7 250 Regulation of cell cycle 74 2.46E−5 203 Protein amino acid 6468 2.48E−5 114 phosphorylation Cytokinesis 910 6.13E−5 165 Cell motility 6928 0.00015 93 Cell cycle 7049 0.00028 138

In Table 2, each of the top 20 over-represented pathways that have the highest frequencies in the 500 signatures of ER-positive and ER-negative tumors (see Table 5) were subjected to Global Test program^(1,2). The Global Test examines the association of a group of genes as a whole to a specific clinical parameter, in this case DMFS, and generates an asymptotic theory P value for the pathway^(1,2). The pathways are ranked by their P value in the respective ER-subgroup of tumors.

The contribution of individual genes in the top over-represented pathways to the association with DMFS, and their significance, were determined for ER-positive (FIG. 5, and Table 5 online) and ER-negative tumors (FIG. 6 online, and Table 6). In these pathways, multiple genes are positively associated with DMFS, indicating a higher expression in tumors without metastatic capability, while other genes show a negative association, indicative of a higher expression in metastatic tumors. In ER-positive tumors such pathways with a mixed association included the top 2 significant pathways Apoptosis (FIG. 2 a) and Regulation of cell cycle (FIG. 2 c). There were also a number of pathways that had dominant positive or negative correlation with DMFS. For example, Immune response of GOBP contains 379 probe sets, of which most showed positive correlation to DMFS (FIG. 2 e). Similarly in Cellular defense response and Chemotaxis, most genes displayed a strong positive correlation with DMFS (FIG. 5 online). On the other hand, genes in Mitosis (FIG. 2 g), Mitotic chromosome segregation, and Cell cycle, showed a dominant negative correlation with DMFS (FIG. 5). Thus, in general the cell division-related pathways have dominant negative correlation with survival time, while immune-related pathways have dominant positive correlation. This indicates that ER-positive tumors with metastatic capability tend to have higher cell division rates and induce lower immune activities from the host body.

TABLE 5 Significant genes in the top 20 pathways for ER-positive tumors Gene PSID influence sd z-score info Symbol Gene Title Apoptosis 208905_at 13.03 3.04 4.29 − CYCS cytochrome c, somatic 202731_at 46.15 11.50 4.01 + PDCD4 programmed cell death 4 204817_at 36.39 9.77 3.73 − ESPL1 extra spindle poles like 1 206150_at 67.60 18.92 3.57 + TNFRSF7 tumor necrosis factor receptor superfamily, member 7 38158_at 24.65 7.23 3.41 − ESPL1 extra spindle poles like 1 202730_s_at 27.75 8.73 3.18 + PDCD4 programmed cell death 4 209539_at 31.06 9.89 3.14 + ARHGEF6 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 212593_s_at 39.35 12.82 3.07 + PDCD4 programmed cell death 4 204947_at 50.65 16.65 3.04 − E2F1 E2F transcription factor 1 201111_at 18.77 6.18 3.04 − CSE1L CSE1 chromosome segregation 1-like 201636_at 6.94 2.34 2.97 − FXR1 fragile X mental retardation, autosomal homolog 1 204933_s_at 133.57 45.18 2.96 + TNFRSF11B tumor necrosis factor receptor superfamily, member 11b 220048_at 3.61 1.28 2.82 − EDAR ectodysplasin A receptor 210766_s_at 12.50 4.54 2.75 − CSE1L CSE1 chromosome segregation 1-like (yeast) 221567_at 18.12 6.81 2.66 − NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) 213829_x_at 6.73 2.54 2.65 − TNFRSF6B tumor necrosis factor receptor superfamily, member 6b, decoy 201112_s_at 7.18 2.79 2.57 − CSE1L CSE1 chromosome segregation 1-like 212353_at 27.06 10.77 2.51 − SULF1 sulfatase 1 208822_s_at 4.48 1.81 2.47 − DAP3 death associated protein 3 209831_x_at 6.29 2.59 2.43 + DNASE2 deoxyribonuclease II, lysosomal 203187_at 7.63 3.21 2.37 + DOCK1 dedicator of cytokinesis 1 209462_at 87.55 36.92 2.37 − APLP1 amyloid beta (A4) precursor-like protein 1 210164_at 54.43 23.24 2.34 + GZMB granzyme B 203005_at 4.52 1.98 2.29 − LTBR lymphotoxin beta receptor 209239_at 8.01 3.57 2.24 + NFKB1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 202535_at 14.80 6.72 2.20 − FADD Fas (TNFRSF6)-associated via death domain 209803_s_at 48.69 22.44 2.17 − PHLDA2 pleckstrin homology-like domain, family A, member 2 204513_s_at 9.17 4.29 2.14 + ELMO1 engulfment and cell motility 1 (ced-12 homolog, C. elegans) 210538_s_at 26.69 12.54 2.13 + BIRC3 baculoviral IAP repeat-containing 3 217840_at 3.44 1.62 2.12 − DDX41 DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 208402_at 34.33 16.37 2.10 + IL17 interleukin 17 (cytotoxic T-lymphocyte- associated serine esterase 8) 214992_s_at 7.20 3.46 2.08 + DNASE2 deoxyribonuclease II, lysosomal 209201_x_at 28.29 13.71 2.06 + CXCR4 chemokine (C—X—C motif) receptor 4 2028_s_at 2.14 1.06 2.01 − E2F1 E2F transcription factor 1 201588_at 1.13 0.56 2.01 − TXNL1 thioredoxin-like 1 203836_s_at 6.48 3.29 1.97 + MAP3K5 mitogen-activated protein kinase kinase kinase 5 215719_x_at 20.18 10.30 1.96 + FAS Fas (TNF receptor superfamily, member 6) Regulation of cell cycle 204817_at 33.18 8.90 3.73 − ESPL1 extra spindle poles like 1 38158_at 22.48 6.60 3.41 − ESPL1 extra spindle poles like 1 214710_s_at 22.24 7.19 3.10 − CCNB1 cyclin B1 201076_at 7.52 2.43 3.09 + NHP2L1 NHP2 non-histone chromosome protein 2-like 1 212426_s_at 7.86 2.55 3.08 − YWHAQ tyrosine 3-monooxygenase/tryptophan 5- monooxygenase activation protein 204009_s_at 7.79 2.53 3.08 − KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 204947_at 46.18 15.18 3.04 − E2F1 E2F transcription factor 1 201947_s_at 7.00 2.30 3.04 − CCT2 chaperonin containing TCP1, subunit 2 (beta) 201601_x_at 24.46 8.16 3.00 + IFITM1 interferon induced transmembrane protein 1 (9- 27) 204822_at 42.21 14.49 2.91 − TTK TTK protein kinase 204015_s_at 71.73 24.75 2.90 + DUSP4 dual specificity phosphatase 4 220407_s_at 17.06 6.36 2.68 + TGFB2 transforming growth factor, beta 2 209096_at 7.11 2.77 2.57 − UBE2V2 ubiquitin-conjugating enzyme E2 variant 2 204826_at 10.95 4.33 2.53 − CCNF cyclin F 212022_s_at 35.48 14.44 2.46 − MKI67 antigen identified by monoclonal antibody Ki-67 202647_s_at 8.26 3.41 2.42 − NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 206404_at 26.09 10.98 2.38 + FGF9 fibroblast growth factor 9 (glia-activating factor) 202705_at 25.47 10.74 2.37 − CCNB2 cyclin B2 202870_s_at 25.76 11.32 2.28 − CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) 205842_s_at 11.21 4.96 2.26 + JAK2 Janus kinase 2 (a protein tyrosine kinase) 214022_s_at 13.99 6.25 2.24 + IFITM1 interferon induced transmembrane protein 1 (9- 27) 211251_x_at 6.21 2.96 2.10 + NFYC nuclear transcription factor Y, gamma 204014_at 48.13 23.03 2.09 + DUSP4 dual specificity phosphatase 4 212781_at 3.04 1.50 2.02 − RBBP6 retinoblastoma binding protein 6 2028_s_at 1.95 0.97 2.01 − E2F1 E2F transcription factor 1 Protein amino acid phosphorylation 208079_s_at 120.73 28.59 4.22 − STK6 serine/threonine kinase 6 204092_s_at 62.39 17.05 3.66 − STK6 serine/threonine kinase 6 204641_at 143.19 40.31 3.55 − NEK2 NIMA (never in mitosis gene a)-related kinase 2 210754_s_at 22.18 6.89 3.22 + LYN v-yes-1 Yamaguchi sarcoma viral related oncogene homolog 218909_at 6.75 2.10 3.21 − RPS6KC1 ribosomal protein S6 kinase, 52 kDa, polypeptide 1 202543_s_at 21.69 6.87 3.16 − GMFB glia maturation factor, beta 204825_at 43.55 13.94 3.12 − MELK maternal embryonic leucine zipper kinase 203213_at 52.80 17.25 3.06 − CDC2 Cell division cycle 2, G1 to S and G2 to M 204822_at 63.55 21.81 2.91 − TTK TTK protein kinase 204171_at 23.52 8.48 2.77 − RPS6KB1 ribosomal protein S6 kinase, 70 kDa, polypeptide 1 218764_at 12.75 4.71 2.71 + PRKCH protein kinase C, eta 216598_s_at 118.88 46.84 2.54 + CCL2 chemokine (C—C motif) ligand 2 203755_at 19.43 7.95 2.44 − BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 208944_at 24.04 9.85 2.44 + TGFBR2 transforming growth factor, beta receptor II (70/80 kDa) 220038_at 46.82 19.30 2.43 + SGK3 serum/glucocorticoid regulated kinase family, member 3 209642_at 33.53 13.87 2.42 − BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) 207957_s_at 73.49 30.64 2.40 + ATP6AP1 ATPase, H+ transporting, lysosomal accessory protein 1 208018_s_at 11.78 5.00 2.36 + HCK hemopoietic cell kinase 212486_s_at 30.72 13.32 2.31 + FYN FYN oncogene related to SRC, FGR, YES 216033_s_at 44.93 19.72 2.28 + FYN FYN oncogene related to SRC, FGR, YES 205842_s_at 16.88 7.47 2.26 + JAK2 Janus kinase 2 (a protein tyrosine kinase) 219813_at 16.04 7.16 2.24 + LATS1 LATS, large tumor suppressor, homolog 1 (Drosophila) 220987_s_at 4.46 2.03 2.19 − NUAK2 NUAK family, SNF1-like kinase, 2 212530_at 3.13 1.44 2.17 − NEK7 NIMA (never in mitosis gene a)-related kinase 7 209282_at 8.49 4.15 2.04 + PRKD2 protein kinase D2 202200_s_at 3.80 1.88 2.02 − SRPK1 SFRS protein kinase 1 203836_s_at 8.90 4.51 1.97 + MAP3K5 mitogen-activated protein kinase kinase kinase 5 Cytokinesis 204817_at 17.44 4.68 3.73 − ESPL1 extra spindle poles like 1 204641_at 49.99 14.07 3.55 − NEK2 NIMA (never in mitosis gene a)-related kinase 2 38158_at 11.82 3.47 3.41 − ESPL1 extra spindle poles like 1 218009_s_at 18.49 5.67 3.26 − PRC1 protein regulator of cytokinesis 1 214710_s_at 11.69 3.78 3.10 − CCNB1 cyclin B1 203213_at 18.43 6.02 3.06 − CDC2 Cell division cycle 2, G1 to S and G2 to M 205046_at 43.34 16.80 2.58 − CENPE centromere protein E, 312 kDa 204826_at 5.76 2.27 2.53 − CCNF cyclin F 201589_at 3.22 1.32 2.44 − SMC1L1 SMC1 structural maintenance of chromosomes 1-like 1 200815_s_at 2.27 0.94 2.41 − PAFAH1B1 platelet-activating factor acetylhydrolase, isoform lb, alpha subunit 45 kDa 202705_at 13.39 5.64 2.37 − CCNB2 cyclin B2 200726_at 1.62 0.70 2.32 − PPP1CC protein phosphatase 1, catalytic subunit, gamma isoform 202870_s_at 13.54 5.95 2.28 − CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) 201897_s_at 3.37 1.58 2.14 − CKS1B CDC28 protein kinase regulatory subunit 1B 204170_s_at 8.07 3.89 2.07 − CKS2 CDC28 protein kinase regulatory subunit 2 213743_at 1.39 0.70 1.99 − CCNT2 cyclin T2 Cell motility 207165_at 35.78 9.04 3.96 − HMMR hyaluronan-mediated motility receptor (RHAMM) 206983_at 32.30 9.85 3.28 + CCR6 chemokine (C—C motif) receptor 6 211719_x_at 5.66 1.97 2.87 − FN1 fibronectin 1 211577_s_at 18.73 7.25 2.58 + IGF1 insulin-like growth factor 1 210495_x_at 3.69 1.49 2.47 − FN1 fibronectin 1 208991_at 5.91 2.43 2.43 + STAT3 signal transducer and activator of transcription 3 200815_s_at 3.18 1.32 2.41 − PAFAH1B1 platelet-activating factor acetylhydrolase, isoform lb, alpha subunit 45 kDa 200973_s_at 10.68 4.50 2.37 + TSPAN3 tetraspanin 3 216442_x_at 3.76 1.65 2.27 − FN1 fibronectin 1 209540_at 25.74 11.37 2.26 + IGF1 insulin-like growth factor 1 (somatomedin C) 205842_s_at 8.27 3.66 2.26 + JAK2 Janus kinase 2 (a protein tyrosine kinase) 209083_at 19.05 8.86 2.15 + CORO1A coronin, actin binding protein, 1A 204513_s_at 6.17 2.89 2.14 + ELMO1 engulfment and cell motility 1 (ced-12 homolog, C. elegans) 207008_at 32.40 15.61 2.08 + IL8RB interleukin 8 receptor, beta 208992_s_at 13.84 6.76 2.05 + STAT3 signal transducer and activator of transcription 3 213101_s_at 2.59 1.28 2.03 − ACTR3 ARP3 actin-related protein 3 homolog (yeast) 208679_s_at 3.77 1.93 1.96 + ARPC2 actin related protein 2/3 complex, subunit 2, 34 kDa Cell cycle 201664_at 18.20 4.00 4.55 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 208079_s_at 84.89 20.10 4.22 − STK6 serine/threonine kinase 6 204092_s_at 43.87 11.99 3.66 − STK6 serine/threonine kinase 6 215623_x_at 16.82 5.18 3.25 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 218663_at 28.34 9.46 2.99 − HCAP-G chromosome condensation protein G 203362_s_at 35.05 12.46 2.81 − MAD2L1 MAD2 mitotic arrest deficient-like 1 32137_at 4.45 1.67 2.67 − JAG2 jagged 2 203755_at 13.66 5.59 2.44 − BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta 201589_at 6.49 2.66 2.44 − SMC1L1 SMC1 structural maintenance of chromosomes 1-like 1 209642_at 23.58 9.75 2.42 − BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog 204496_at 11.23 4.77 2.35 − STRN3 striatin, calmodulin binding protein 3 218662_s_at 10.87 4.96 2.19 − HCAP-G chromosome condensation protein G 201663_s_at 8.91 4.21 2.12 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 204170_s_at 16.25 7.83 2.07 − CKS2 CDC28 protein kinase regulatory subunit 2 206499_s_at 3.35 1.62 2.07 + RCC1 regulator of chromosome condensation 1 202214_s_at 2.35 1.16 2.03 + CUL4B cullin 4B 213743_at 2.80 1.41 1.99 − CCNT2 cyclin T2 Cell surface receptor linked signal transduction 206150_at 36.90 10.33 3.57 + TNFRSF7 tumor necrosis factor receptor superfamily, member 7 205926_at 9.28 2.66 3.49 + IL27RA interleukin 27 receptor, alpha 212587_s_at 23.07 6.96 3.32 + PTPRC protein tyrosine phosphatase, receptor type, C 201601_x_at 14.65 4.89 3.00 + IFITM1 interferon induced transmembrane protein 1 (9- 27) 211000_s_at 12.04 4.40 2.73 + IL6ST interleukin 6 signal transducer (gp130, oncostatin M receptor) 214470_at 33.53 13.03 2.57 + KLRB1 killer cell lectin-like receptor subfamily B, member 1 222062_at 29.79 12.76 2.33 + IL27RA interleukin 27 receptor, alpha 214022_s_at 8.38 3.74 2.24 + IFITM1 interferon induced transmembrane protein 1 (9- 27) 202535_at 8.08 3.67 2.20 − FADD Fas (TNFRSF6)-associated via death domain 210538_s_at 14.57 6.84 2.13 + BIRC3 baculoviral IAP repeat-containing 3 Mitosis 201664_at 8.10 1.78 4.55 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 208079_s_at 37.77 8.94 4.22 − STK6 serine/threonine kinase 6 204092_s_at 19.52 5.33 3.66 − STK6 serine/threonine kinase 6 215623_x_at 7.48 2.31 3.25 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 209172_s_at 9.26 2.86 3.24 − CENPF centromere protein F, 350/400ka (mitosin) 214710_s_at 10.47 3.38 3.10 − CCNB1 cyclin B1 203213_at 16.52 5.40 3.06 − CDC2 Cell division cycle 2, G1 to S and G2 to M 218663_at 12.61 4.21 2.99 − HCAP-G chromosome condensation protein G 203362_s_at 15.59 5.55 2.81 − MAD2L1 MAD2 mitotic arrest deficient-like 1 204826_at 5.16 2.04 2.53 − CCNF cyclin F 203755_at 6.08 2.49 2.44 − BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta 209642_at 10.49 4.34 2.42 − BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog 200815_s_at 2.03 0.84 2.41 − PAFAH1B1 platelet-activating factor acetylhydrolase, isoform lb, alpha subunit 45 kDa 202705_at 12.00 5.06 2.37 − CCNB2 cyclin B2 209408_at 6.66 2.87 2.32 − KIF2C kinesin family member 2C 202870_s_at 12.13 5.33 2.28 − CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) 218662_s_at 4.83 2.21 2.19 − HCAP-G chromosome condensation protein G 209083_at 12.16 5.65 2.15 + CORO1A coronin, actin binding protein, 1A 201663_s_at 3.97 1.87 2.12 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 206499_s_at 1.49 0.72 2.07 + RCC1 regulator of chromosome condensation 1 Intracellular protein transport 201216_at 22.62 4.46 5.07 + ERP29 endoplasmic reticulum protein 29 211779_x_at 10.48 3.08 3.40 + AP2A2 adaptor-related protein complex 2, alpha 2 subunit 212159_x_at 11.53 3.60 3.21 + AP2A2 adaptor-related protein complex 2, alpha 2 subunit 201088_at 51.35 16.82 3.05 − KPNA2 karyopherin alpha 2 201111_at 32.61 10.74 3.04 − CSE1L CSE1 chromosome segregation 1-like 204478_s_at 9.39 3.13 3.00 − RABIF RAB interacting factor 203311_s_at 15.15 5.20 2.91 + ARF6 ADP-ribosylation factor 6 214337_at 105.30 36.24 2.91 − COPA coatomer protein complex, subunit alpha 204974_at 52.86 18.62 2.84 − RAB3A RAB3A, member RAS oncogene family 202630_at 22.63 8.05 2.81 − APPBP2 amyloid beta precursor protein (cytoplasmic tail) binding protein 2 208819_at 4.68 1.68 2.78 + RAB8A RAB8A, member RAS oncogene family 210766_s_at 21.71 7.89 2.75 − CSE1L CSE1 chromosome segregation 1-like 209268_at 9.70 3.53 2.74 − VPS45A vacuolar protein sorting 45A 201831_s_at 9.56 3.50 2.73 + VDP vesicle docking protein p115 218360_at 16.60 6.43 2.58 − RAB22A RAB22A, member RAS oncogene family 201112_s_at 12.48 4.85 2.57 − CSE1L CSE1 chromosome segregation 1-like 203679_at 11.96 4.69 2.55 + TMED1 transmembrane emp24 protein transport domain containing 1 218755_at 32.63 12.95 2.52 − KIF20A kinesin family member 20A 209238_at 12.00 4.78 2.51 − STX3A syntaxin 3A 204017_at 24.75 10.31 2.40 − KDELR3 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3 202395_at 16.99 7.11 2.39 − NSF N-ethylmaleimide-sensitive factor 221014_s_at 7.83 3.53 2.22 − RAB33B RAB33B, member RAS oncogene family 212652_s_at 3.70 1.73 2.14 − SNX4 sorting nexin 4 212103_at 4.16 1.95 2.13 + KPNA6 Karyopherin alpha 6 (importin alpha 7) 204477_at 9.92 4.67 2.13 − RABIF RAB interacting factor 201097_s_at 2.72 1.28 2.12 − ARF4 ADP-ribosylation factor 4 212635_at 6.06 2.88 2.10 − TNPO1 Transportin 1 203544_s_at 8.14 3.93 2.07 − STAM signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 211762_s_at 19.76 9.65 2.05 − KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) 200614_at 11.87 5.87 2.02 − CLTC clathrin, heavy polypeptide (Hc) 208732_at 8.12 4.07 2.00 − RAB2 RAB2, member RAS oncogene family 200699_at 8.38 4.29 1.95 − KDELR2 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 Mitotic chromosome segregation 201664_at 6.77 1.49 4.55 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 204817_at 13.07 3.51 3.73 − ESPL1 extra spindle poles like 1 38158_at 8.85 2.60 3.41 − ESPL1 extra spindle poles like 1 215623_x_at 6.26 1.93 3.25 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 201589_at 2.41 0.99 2.44 − SMC1L1 SMC1 structural maintenance of chromosomes 1-like 1 201663_s_at 3.32 1.57 2.12 − SMC4L1 SMC4 structural maintenance of chromosomes 4-like 1 Ubiquitin-dependent protein catabolism 201178_at 10.32 2.73 3.79 + FBXO7 F-box protein 7 202244_at 9.40 2.71 3.48 − PSMB4 proteasome (prosome, macropain) subunit, beta type, 4 211702_s_at 20.08 7.60 2.64 − USP32 ubiquitin specific peptidase 32 221519_at 5.75 2.22 2.58 + FBXW4 F-box and WD-40 domain protein 4 202981_x_at 9.35 3.90 2.40 − SIAH1 seven in absentia homolog 1 (Drosophila) 209040_s_at 46.23 19.42 2.38 + PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 208805_at 11.48 4.83 2.38 − PSMA6 proteasome (prosome, macropain) subunit, alpha type, 6 202243_s_at 6.60 2.87 2.30 − PSMB4 proteasome (prosome, macropain) subunit, beta type, 4 202870_s_at 46.10 20.26 2.28 − CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) 208760_at 10.11 4.70 2.15 − UBE2I Ubiquitin-conjugating enzyme E2I 201317_s_at 5.90 2.77 2.13 − PSMA2 proteasome (prosome, macropain) subunit, alpha type, 2 DNA repair 219510_at 16.77 4.57 3.67 − POLQ polymerase (DNA directed), theta 213520_at 157.23 44.55 3.53 − RECQL4 RecQ protein-like 4 219502_at 12.24 4.08 3.00 − NEIL3 nei endonuclease VIII-like 3 204146_at 29.05 10.24 2.84 − RAD51AP1 RAD51 associated protein 1 204558_at 53.36 20.63 2.59 − RAD54L RAD54-like 204531_s_at 11.12 4.52 2.46 − BRCA1 breast cancer 1, early onset 201589_at 5.45 2.23 2.44 − SMC1L1 SMC1 structural maintenance of chromosomes 1-like 1 218397_at 5.64 2.56 2.21 − FANCL Fanconi anemia, complementation group L 213734_at 6.10 2.79 2.18 − WSB2 WD repeat and SOCS box-containing 2 Induction of apoptosis 208905_at 14.07 3.28 4.29 − CYCS cytochrome c, somatic 206150_at 72.98 20.43 3.57 + TNFRSF7 tumor necrosis factor receptor superfamily, member 7 209448_at 24.65 11.28 2.19 − HTATIP2 HIV-1 Tat interactive protein 2, 30 kDa 209929_s_at 4.91 2.49 1.97 − IKBKG inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma 215719_x_at 21.79 11.12 1.96 + FAS Fas (TNF receptor superfamily, member 6) Immune response 206150_at 22.64 6.34 3.57 + TNFRSF7 tumor necrosis factor receptor superfamily, member 7 215633_x_at 17.75 5.04 3.52 + LST1 leukocyte specific transcript 1 205926_at 5.69 1.63 3.49 + IL27RA interleukin 27 receptor, alpha 210629_x_at 7.36 2.12 3.47 + LST1 leukocyte specific transcript 1 204670_x_at 13.15 3.95 3.33 + HLA-DRB1 major histocompatibility complex, class II, DR beta 1 211582_x_at 17.49 5.72 3.06 + LST1 leukocyte specific transcript 1 210982_s_at 31.37 10.27 3.05 + HLA-DRA major histocompatibility complex, class II, DR alpha 209312_x_at 13.65 4.51 3.02 + HLA-DRB1 major histocompatibility complex, class II, DR beta 1 213226_at 10.10 3.37 3.00 − CCNA2 Cyclin A2 201601_x_at 8.98 3.00 3.00 + IFITM1 interferon induced transmembrane protein 1 (9-27) 208894_at 24.35 8.56 2.84 + HLA-DRA major histocompatibility complex, class II, DR alpha 211991_s_at 17.17 6.07 2.83 + HLA-DPA1 major histocompatibility complex, class II, DP alpha 1 215193_x_at 17.46 6.18 2.82 + HLA-DRB1 major histocompatibility complex, class II, DR beta 1 217478_s_at 9.71 3.45 2.82 + HLA-DMA major histocompatibility complex, class II, DM alpha 210072_at 31.12 11.12 2.80 + CCL19 chemokine (C—C motif) ligand 19 200904_at 8.21 2.98 2.76 + HLA-E major histocompatibility complex, class I, E 211000_s_at 7.38 2.70 2.73 + IL6ST interleukin 6 signal transducer (gp130, oncostatin M receptor) 211581_x_at 12.05 4.50 2.68 + LST1 leukocyte specific transcript 1 209823_x_at 21.88 8.17 2.68 + HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 207850_at 17.82 6.79 2.63 + CXCL3 chemokine (C—X—C motif) ligand 3 208306_x_at 8.90 3.40 2.62 + HLA-DRB1 Major histocompatibility complex, class II, DR beta 3 203010_at 3.23 1.27 2.54 + STAT5A signal transducer and activator of transcription 5A 200905_x_at 3.98 1.58 2.52 + HLA-E major histocompatibility complex, class I, E 201288_at 6.88 2.73 2.52 + ARHGDIB Rho GDP dissociation inhibitor (GDI) beta 215784_at 30.48 12.17 2.50 + CD1E CD1E antigen, e polypeptide 205544_s_at 26.20 10.46 2.50 + CR2 complement component (3d/Epstein Barr virus) receptor 2 211430_s_at 23.54 9.63 2.44 + IGH immunoglobulin heavy constant gamma 1 (G1m marker) 217456_x_at 2.67 1.09 2.44 + HLA-E major histocompatibility complex, class I, E 201137_s_at 8.17 3.36 2.43 + HLA-DPB1 major histocompatibility complex, class II, DP beta 1 211529_x_at 7.99 3.32 2.41 + HLA-G HLA-G histocompatibility antigen, class I, G 212592_at 42.76 17.85 2.40 + IGJ Immunoglobulin J polypeptide 204470_at 7.85 3.30 2.38 + CXCL1 chemokine (C—X—C motif) ligand 1 209040_s_at 9.49 3.99 2.38 + PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 209687_at 14.05 5.97 2.35 + CXCL12 chemokine (C—X—C motif) ligand 12 222062_at 18.27 7.83 2.33 + IL27RA interleukin 27 receptor, alpha 205671_s_at 14.74 6.33 2.33 + HLA-DOB major histocompatibility complex, class II, DO beta 202748_at 4.75 2.04 2.33 + GBP2 guanylate binding protein 2, interferon-inducible 217767_at 12.27 5.31 2.31 + C3 complement component 3 211799_x_at 9.65 4.19 2.30 + HLA-C major histocompatibility complex, class I, C 203005_at 1.51 0.66 2.29 − LTBR lymphotoxin beta receptor (TNFR superfamily, member 3) 212203_x_at 2.79 1.22 2.28 + IFITM3 interferon induced transmembrane protein 3 (1-8 U) 203666_at 5.48 2.43 2.26 + CXCL12 chemokine (C—X—C motif) ligand 12 214022_s_at 5.14 2.30 2.24 + IFITM1 interferon induced transmembrane protein 1 (9-27) 217014_s_at 15.72 7.03 2.24 + AZGP1 alpha-2-glycoprotein 1, zinc 211911_x_at 8.34 3.73 2.23 + HLA-B major histocompatibility complex, class I, B 210514_x_at 11.98 5.36 2.23 + HLA-G HLA-G histocompatibility antigen, class I, G 204116_at 6.74 3.09 2.18 + IL2RG interleukin 2 receptor, gamma 209619_at 8.17 3.75 2.18 + CD74 CD74 antigen 208729_x_at 7.58 3.54 2.14 + HLA-B major histocompatibility complex, class I, B 207323_s_at 2.28 1.08 2.12 + MBP myelin basic protein 212671_s_at 15.09 7.13 2.12 + HLA-DQA1 major histocompatibility complex, class II, DQ /// HLA- alpha 1 DQA2 211528_x_at 6.34 3.00 2.11 + HLA-G HLA-G histocompatibility antigen, class I, G 208402_at 11.50 5.48 2.10 + IL17 interleukin 17 209666_s_at 2.11 1.01 2.08 − CHUK conserved helix-loop-helix ubiquitous kinase 209201_x_at 9.47 4.59 2.06 + CXCR4 chemokine (C—X—C motif) receptor 4 206641_at 23.27 11.37 2.05 + TNFRSF17 tumor necrosis factor receptor superfamily, member 17 211734_s_at 12.74 6.25 2.04 + FCER1A Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide 204806_x_at 4.70 2.33 2.02 + HLA-F major histocompatibility complex, class I, F 215669_at 3.81 1.90 2.01 − HLA-DRB4 major histocompatibility complex, class II, DR beta 4 206086_x_at 0.71 0.36 1.98 − HFE hemochromatosis 209929_s_at 1.52 0.77 1.97 − IKBKG inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma 202992_at 25.86 13.15 1.97 + C7 complement component 7 214974_x_at 8.97 4.58 1.96 + CXCL5 chemokine (C—X—C motif) ligand 5 215719_x_at 6.76 3.45 1.96 + FAS Fas (TNF receptor superfamily, member 6) Protein biosynthesis 211666_x_at 56.18 14.56 3.86 + RPL3 ribosomal protein L3 217747_s_at 21.97 6.01 3.66 + RPS9 ribosomal protein S9 200937_s_at 22.70 6.32 3.59 + RPL5 ribosomal protein L5 200081_s_at 18.99 5.85 3.25 + RPS6 ribosomal protein S6 201076_at 18.95 6.12 3.09 + NHP2L1 NHP2 non-histone chromosome protein 2-like 1 211938_at 17.38 5.67 3.07 + EIF4B eukaryotic translation initiation factor 4B 200024_at 20.65 6.95 2.97 + RPS5 ribosomal protein S5 208887_at 22.22 7.58 2.93 + EIF3S4 eukaryotic translation initiation factor 3, subunit 4 delta, 44 kDa 213687_s_at 7.25 2.48 2.92 + RPL35A ribosomal protein L35a 200036_s_at 13.18 4.52 2.91 + RPL10A ribosomal protein L10a 200823_x_at 46.07 15.87 2.90 + RPL29 ribosomal protein L29 220960_x_at 20.05 7.47 2.68 + RPL22 ribosomal protein L22 211710_x_at 6.88 2.58 2.66 + RPL4 ribosomal protein L4 202247_s_at 16.72 6.28 2.66 + MTA1 metastasis associated 1 200005_at 8.27 3.11 2.66 + EIF3S7 eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67 kDa 200013_at 4.18 1.59 2.63 + RPL24 ribosomal protein L24 221726_at 12.88 4.90 2.63 + RPL22 ribosomal protein L22 201258_at 6.53 2.49 2.62 + RPS16 ribosomal protein S16 213310_at 34.83 13.70 2.54 − EIF2C2 Eukaryotic translation initiation factor 2C, 2 200074_s_at 11.82 4.67 2.53 + RPL14 ribosomal protein L14 200869_at 29.52 11.75 2.51 + RPL18A ribosomal protein L18a 218270_at 7.18 2.92 2.46 + MRPL24 mitochondrial ribosomal protein L24 209609_s_at 10.14 4.22 2.40 − MRPL9 mitochondrial ribosomal protein L9 201254_x_at 2.75 1.19 2.31 + RPS6 ribosomal protein S6 201154_x_at 5.49 2.40 2.29 + RPL4 ribosomal protein L4 200010_at 5.97 2.63 2.27 + RPL11 Ribosomal protein L11 201064_s_at 7.61 3.38 2.25 + PABPC4 poly(A) binding protein, cytoplasmic 4 (inducible form) 200022_at 8.61 3.89 2.21 + RPL18 ribosomal protein L18 212450_at 10.26 4.66 2.20 − KIAA0256 KIAA0256 gene product 213414_s_at 3.95 1.83 2.16 + RPS19 ribosomal protein S19 221798_x_at 0.88 0.41 2.16 − RPS2 Ribosomal protein S2 211937_at 8.65 4.05 2.14 + EIF4B eukaryotic translation initiation factor 4B 208264_s_at 8.58 4.08 2.10 − EIF3S1 eukaryotic translation initiation factor 3, subunit 1 alpha, 35 kDa 200012_x_at 8.42 4.04 2.08 + RPL21 ribosomal protein L21 200858_s_at 5.06 2.44 2.07 + RPS8 ribosomal protein S8 209134_s_at 3.91 1.95 2.01 + RPS6 ribosomal protein S6 208695_s_at 0.96 0.49 1.97 − RPL39 ribosomal protein L39 DNA replication 219105_x_at 18.23 5.57 3.27 − ORC6L origin recognition complex, subunit 6 homolog- like 201890_at 37.16 11.68 3.18 − RRM2 ribonucleotide reductase M2 polypeptide 211577_s_at 20.37 7.88 2.58 + IGF1 insulin-like growth factor 1 (somatomedin C) 221521_s_at 44.39 17.27 2.57 − Pfs2 DNA replication complex GINS protein PSF2 209773_s_at 17.73 7.37 2.40 − RRM2 ribonucleotide reductase M2 polypeptide 209540_at 27.99 12.37 2.26 + IGF1 insulin-like growth factor 1 (somatomedin C) 213033_s_at 24.87 11.15 2.23 + NFIB Nuclear factor I/B 213734_at 5.51 2.52 2.18 − WSB2 WD repeat and SOCS box-containing 2 204767_s_at 7.16 3.28 2.18 − FEN1 flap structure-specific endonuclease 1 204127_at 3.68 1.82 2.02 − RFC3 replication factor C (activator 1) 3, 38 kDa 208752_x_at 1.16 0.59 1.97 + NAP1L1 nucleosome assembly protein 1-like 1 Oncogenesis 208079_s_at 83.78 19.84 4.22 − STK6 serine/threonine kinase 6 204092_s_at 43.30 11.83 3.66 − STK6 serine/threonine kinase 6 213829_x_at 6.41 2.42 2.65 − TNFRSF6B tumor necrosis factor receptor superfamily, member 6b, decoy 206413_s_at 36.36 14.96 2.43 − TCL1B T-cell leukemia/lymphoma 1B 203035_s_at 7.62 3.14 2.42 − PIAS3 protein inhibitor of activated STAT, 3 202095_s_at 51.32 21.44 2.39 − BIRC5 baculoviral IAP repeat-containing 5 (survivin) 210434_x_at 3.61 1.54 2.34 − JTB jumping translocation breakpoint 209054_s_at 3.75 1.81 2.08 − WHSC1 Wolf-Hirschhorn syndrome candidate 1 200048_s_at 2.32 1.14 2.04 − JTB jumping translocation breakpoint 203554_x_at 9.16 4.61 1.98 − PTTG1 pituitary tumor-transforming 1 203192_at 5.92 3.01 1.97 − ABCB6 ATP-binding cassette, sub-family B (MDR/TAP), member 6 Metabolism 212070_at 41.12 14.17 2.90 − GPR56 G protein-coupled receptor 56 221256_s_at 21.39 7.39 2.89 + HDHD3 haloacid dehalogenase-like hydrolase domain containing 3 203067_at 13.34 4.66 2.86 − PDHX pyruvate dehydrogenase complex, component X 212062_at 35.52 12.70 2.80 − ATP9A ATPase, Class II, type 9A 202651_at 17.67 6.42 2.75 − LPGAT1 lysophosphatidylglycerol acyltransferase 1 220892_s_at 25.32 9.50 2.67 + PSAT1 phosphoserine aminotransferase 1 206335_at 9.17 3.62 2.53 − GALNS galactosamine (N-acetyl)-6-sulfate sulfatase 202722_s_at 16.76 6.66 2.51 − GFPT1 glutamine-fructose-6-phosphate transaminase 1 212353_at 45.42 18.09 2.51 − SULF1 sulfatase 1 221928_at 39.21 16.23 2.42 + ACACB acetyl-Coenzyme A carboxylase beta 219616_at 10.26 4.30 2.39 − FLJ21963 FLJ21963 protein 202464_s_at 48.50 20.47 2.37 − PFKFB3 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 59705_at 9.15 3.93 2.33 − SCLY selenocysteine lyase 217776_at 21.38 9.75 2.19 − RDH11 retinol dehydrogenase 11 218025_s_at 9.02 4.32 2.09 + PECI peroxisomal D3,D2-enoyl-CoA isomerase 209935_at 12.20 5.92 2.06 − ATP2C1 ATPase, Ca++ transporting, type 2C, member 1 200824_at 31.66 15.69 2.02 + GSTP1 glutathione S-transferase pi 201626_at 4.32 2.15 2.01 − INSIG1 insulin induced gene 1 Cellular defense response 215633_x_at 13.89 3.94 3.52 + LST1 leukocyte specific transcript 1 210629_x_at 5.76 1.66 3.47 + LST1 leukocyte specific transcript 1 206983_at 12.57 3.83 3.28 + CCR6 chemokine (C—C motif) receptor 6 211582_x_at 13.68 4.48 3.06 + LST1 leukocyte specific transcript 1 211581_x_at 9.43 3.52 2.68 + LST1 leukocyte specific transcript 1 210116_at 21.00 8.06 2.61 + SH2D1A SH2 domain protein 1A, Duncan's disease 211529_x_at 6.25 2.59 2.41 + HLA-G HLA-G histocompatibility antigen, class I, G 210514_x_at 9.37 4.20 2.23 + HLA-G HLA-G histocompatibility antigen, class I, G 211528_x_at 4.96 2.35 2.11 + HLA-G HLA-G histocompatibility antigen, class I, G 207008_at 12.62 6.08 2.08 + IL8RB interleukin 8 receptor, beta 206978_at 4.21 2.05 2.05 + CCR2 chemokine (C—C motif) receptor 2 211567_at 10.37 5.27 1.97 + — — 205495_s_at 7.10 3.63 1.96 + GNLY granulysin Chemotaxis 206983_at 15.76 4.80 3.28 + CCR6 chemokine (C—C motif) receptor 6 210072_at 30.51 10.90 2.80 + CCL19 chemokine (C—C motif) ligand 19 207850_at 17.47 6.65 2.63 + CXCL3 chemokine (C—X—C motif) ligand 3 216598_s_at 28.42 11.20 2.54 + CCL2 chemokine (C—C motif) ligand 2 214435_x_at 4.34 1.82 2.39 − RALA v-ral simian leukemia viral oncogene homolog A (ras related) 204470_at 7.69 3.23 2.38 + CXCL1 chemokine (C—X—C motif) ligand 1 209687_at 13.77 5.85 2.35 + CXCL12 chemokine (C—X—C motif) ligand 12 (stromal cell- derived factor 1) 203666_at 5.37 2.38 2.26 + CXCL12 chemokine (C—X—C motif) ligand 12 (stromal cell- derived factor 1) 207008_at 15.81 7.61 2.08 + IL8RB interleukin 8 receptor, beta 209201_x_at 9.29 4.50 2.06 + CXCR4 chemokine (C—X—C motif) receptor 4 206978_at 5.28 2.57 2.05 + CCR2 chemokine (C—C motif) receptor 2 206337_at 6.09 3.06 1.99 + CCR7 chemokine (C—C motif) receptor 7 211567_at 13.00 6.60 1.97 + — — 214974_x_at 8.80 4.49 1.96 + CXCL5 chemokine (C—X—C motif) ligand 5

TABLE 6 significant genes in the top ten pathways for ER negative tumors Gene PSID influence sd z-score info Symbol Gene Title Regulation of cell growth 209648_x_at 23.16 5.77 4.01 − SOCS5 suppressor of cytokine signaling 5 208127_s_at 13.90 3.71 3.75 − SOCS5 suppressor of cytokine signaling 5 209550_at 18.66 5.88 3.18 − NDN necdin homolog (mouse) 201162_at 16.18 5.15 3.14 − IGFBP7 insulin-like growth factor binding protein 7 212279_at 13.20 4.53 2.91 + MAC30 hypothetical protein MAC30 213337_s_at 7.30 2.53 2.88 + SOCS1 suppressor of cytokine signaling 1 213910_at 37.27 12.99 2.87 − IGFBP7 insulin-like growth factor binding protein 7 217982_s_at 3.33 1.20 2.78 − MORF4L1 mortality factor 4 like 1 201185_at 10.66 3.90 2.73 − HTRA1 HtrA serine peptidase 1 209101_at 18.31 6.81 2.69 − CTGF connective tissue growth factor 202149_at 12.23 5.12 2.39 − NEDD9 neural precursor cell expressed, developmentally down-regulated 9 201163_s_at 3.89 1.69 2.31 − IGFBP7 insulin-like growth factor binding protein 7 208394_x_at 4.40 2.07 2.12 − ESM1 endothelial cell-specific molecule 1 211513_s_at 23.97 11.32 2.12 + OGFR opioid growth factor receptor 211512_s_at 4.18 2.11 1.98 + OGFR opioid growth factor receptor Regulation of G-protein coupled receptor signaling pathway 204337_at 31.44 7.89 3.99 − RGS4 regulator of G-protein signalling 4 209324_s_at 10.18 2.73 3.73 − RGS16 regulator of G-protein signalling 16 220300_at 9.44 3.61 2.61 − RGS3 regulator of G-protein signalling 3 202388_at 24.64 9.45 2.61 − RGS2 regulator of G-protein signalling 2, 24 kDa 204396_s_at 5.77 2.47 2.34 − GRK5 G protein-coupled receptor kinase 5 Skeletal development 217404_s_at 199.74 50.77 3.93 − COL2A1 collagen, type II, alpha 1 210135_s_at 14.72 4.62 3.19 − SHOX2 short stature homeobox 2 205941_s_at 14.81 5.41 2.74 − COL10A1 collagen, type X, alpha 1 201792_at 8.36 3.08 2.72 − AEBP1 AE binding protein 1 206091_at 25.05 9.62 2.60 − MATN3 matrilin 3 208443_x_at 18.61 7.88 2.36 − SHOX2 short stature homeobox 2 213943_at 3.30 1.48 2.23 − TWIST1 twist homolog 1(Drosophila) 220076_at 15.77 7.23 2.18 − ANKH ankylosis, progressive homolog (mouse) 210427_x_at 1.45 0.69 2.10 − ANXA2 annexin A2 210809_s_at 3.36 1.64 2.05 − POSTN periostin, osteoblast specific factor 210973_s_at 12.86 6.33 2.03 + FGFR1 fibroblast growth factor receptor 1 213503_x_at 1.24 0.64 1.96 − ANXA2 annexin A2 Protein amino acid phosphorylation 213595_s_at 70.67 19.13 3.69 − CDC42BPA CDC42 binding protein kinase alpha (DMPK- like) 215050_x_at 47.49 13.74 3.46 + MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 208875_s_at 10.32 3.05 3.39 + PAK2 p21 (CDKN1A)-activated kinase 2 216711_s_at 12.50 3.71 3.37 + TAF1 TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor 203131_at 24.32 7.64 3.18 − PDGFRA platelet-derived growth factor receptor, alpha polypeptide 214683_s_at 32.74 10.72 3.05 − CLK1 CDC-like kinase 1 201401_s_at 103.31 33.85 3.05 + ADRBK1 adrenergic, beta, receptor kinase 1 203552_at 12.54 4.52 2.77 − MAP4K5 mitogen-activated protein kinase kinase kinase kinase 5 205880_at 6.18 2.31 2.68 − PRKD1 protein kinase D1 200604_s_at 20.81 8.27 2.52 + PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha 207239_s_at 19.06 7.73 2.47 + PCTK1 PCTAIRE protein kinase 1 214007_s_at 60.27 24.46 2.46 + PTK9 PTK9 protein tyrosine kinase 9 212530_at 8.39 3.43 2.45 − NEK7 NIMA (never in mitosis gene a)-related kinase 7 212740_at 5.21 2.15 2.43 − PIK3R4 phosphoinositide-3-kinase, regulatory subunit 4, p150 215296_at 42.64 17.82 2.39 − CDC42BPA CDC42 binding protein kinase alpha (DMPK- like) 201461_s_at 20.08 8.57 2.34 + MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 204396_s_at 13.51 5.78 2.34 − GRK5 G protein-coupled receptor kinase 5 207667_s_at 14.58 6.35 2.30 + MAP2K3 mitogen-activated protein kinase kinase 3 202127_at 10.85 4.86 2.23 − PRPF4B PRP4 pre-mRNA processing factor 4 homolog B (yeast) 59644_at 9.95 4.50 2.21 − BMP2K BMP2 inducible kinase 207228_at 15.38 6.96 2.21 + PRKACG protein kinase, cAMP-dependent, catalytic, gamma 213490_s_at 43.56 20.23 2.15 + MAP2K2 mitogen-activated protein kinase kinase 2 211599_x_at 8.19 3.83 2.14 + MET met proto-oncogene (hepatocyte growth factor receptor) 211208_s_at 7.35 3.44 2.14 + CASK calcium/calmodulin-dependent serine protein kinase (MAGUK family) 205578_at 20.67 9.69 2.13 − ROR2 receptor tyrosine kinase-like orphan receptor 2 204813_at 6.64 3.30 2.01 + MAPK10 mitogen-activated protein kinase 10 208824_x_at 12.76 6.35 2.01 + PCTK1 PCTAIRE protein kinase 1 Cell adhesion 212724_at 22.05 6.48 3.40 − RND3 Rho family GTPase 3 209210_s_at 26.72 8.13 3.28 − PLEKHC1 pleckstrin homology domain containing, family C member 1 202363_at 24.96 7.95 3.14 − SPOCK sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 209651_at 15.39 4.94 3.12 − TGFB1I1 transforming growth factor beta 1 induced transcript 1 201505_at 21.00 7.24 2.90 − LAMB1 laminin, beta 1 200771_at 8.56 3.01 2.84 − LAMC1 laminin, gamma 1 (formerly LAMB2) 213790_at 14.02 4.96 2.83 − ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 203083_at 12.25 4.39 2.79 − THBS2 thrombospondin 2 222020_s_at 62.24 22.64 2.75 − HNT neurotrimin 205532_s_at 42.40 15.54 2.73 + CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 201792_at 18.97 6.98 2.72 − AEBP1 AE binding protein 1 209101_at 19.18 7.13 2.69 − CTGF connective tissue growth factor 215904_at 29.42 11.01 2.67 + MLLT4 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 201561_s_at 6.71 2.62 2.56 + CLSTN1 calsyntenin 1 204677_at 11.48 4.53 2.53 − CDH5 cadherin 5, type 2, VE-cadherin (vascular epithelium) 214212_x_at 10.68 4.26 2.51 − PLEKHC1 pleckstrin homology domain containing, family C (with FERM domain) member 1 214375_at 23.91 10.02 2.39 − PPFIBP1 PTPRF interacting protein, binding protein 1 (liprin beta 1) 202149_at 12.81 5.37 2.39 − NEDD9 neural precursor cell expressed, developmentally down-regulated 9 204955_at 12.74 5.34 2.39 − SRPX sushi-repeat-containing protein, X-linked 209873_s_at 11.75 5.14 2.29 + PKP3 plakophilin 3 211208_s_at 5.66 2.65 2.14 + CASK calcium/calmodulin-dependent serine protein kinase (MAGUK family) 205176_s_at 3.87 1.82 2.13 − ITGB3BP integrin beta 3 binding protein (beta3- endonexin) 201281_at 2.86 1.39 2.06 + ADRM1 adhesion regulating molecule 1 212843_at 22.00 10.69 2.06 − NCAM1 neural cell adhesion molecule 1 210809_s_at 7.63 3.72 2.05 − POSTN periostin, osteoblast specific factor 205656_at 4.03 1.96 2.05 − PCDH17 protocadherin 17 201438_at 5.86 2.89 2.03 − COL6A3 collagen, type VI, alpha 3 213241_at 6.19 3.06 2.02 − PLXNC1 plexin C1 218975_at 26.96 13.55 1.99 − COL5A3 collagen, type V, alpha 3 Carbohydrate metabolism 202499_s_at 39.16 13.68 2.86 − SLC2A3 solute carrier family 2 (facilitated glucose transporter), member 3 216010_x_at 91.48 32.31 2.83 + FUT3 fucosyltransferase 3 205799_s_at 17.32 6.72 2.58 + SLC3A1 solute carrier family 3, member 1 201765_s_at 4.24 2.08 2.04 + HEXA hexosaminidase A (alpha polypeptide) Nuclear mRNA splicing, via splicesome 200686_s_at 20.80 5.76 3.61 − SFRS11 splicing factor, arginine/serine-rich 11 203376_at 7.88 2.58 3.06 − CDC40 cell division cycle 40 homolog (yeast) 209162_s_at 45.77 16.98 2.69 + PRPF4 PRP4 pre-mRNA processing factor 4 homolog (yeast) 201698_s_at 3.64 1.44 2.52 + SFRS9 splicing factor, arginine/serine-rich 9 200685_at 17.74 7.38 2.40 − SFRS11 splicing factor, arginine/serine-rich 11 202127_at 10.16 4.55 2.23 − PRPF4B PRP4 pre-mRNA processing factor 4 homolog B (yeast) 221546_at 31.79 14.83 2.14 + PRPF18 PRP18 pre-mRNA processing factor 18 homolog (yeast) 201385_at 3.45 1.66 2.08 − DHX15 DEAH (Asp-Glu-Ala-His) box polypeptide 15 204064_at 7.66 3.76 2.04 − THOC1 THO complex 1 214016_s_at 8.09 4.04 2.00 − SFPQ Splicing factor proline/glutamine-rich 219119_at 3.44 1.75 1.97 − LSM8 LSM8 homolog, U6 small nuclear RNA associated Signal transduction 204337_at 77.97 19.56 3.99 − RGS4 regulator of G-protein signalling 4 209324_s_at 25.24 6.77 3.73 − RGS16 regulator of G-protein signalling 16 204464_s_at 14.07 3.89 3.62 − EDNRA endothelin receptor type A 202247_s_at 14.76 4.24 3.48 + MTA1 metastasis associated 1 221773_at 16.08 4.70 3.42 − ELK3 ELK3, ETS-domain protein (SRF accessory protein 2) 203328_x_at 3.87 1.13 3.41 + IDE insulin-degrading enzyme 208875_s_at 10.94 3.23 3.39 + PAK2 p21 (CDKN1A)-activated kinase 2 201835_s_at 19.43 6.22 3.12 + PRKAB1 protein kinase, AMP-activated, beta 1 non- catalytic subunit 217496_s_at 6.53 2.13 3.07 + IDE insulin-degrading enzyme 209895_at 64.80 21.23 3.05 + PTPN11 protein tyrosine phosphatase, non-receptor type 11 201401_s_at 109.49 35.88 3.05 + ADRBK1 adrenergic, beta, receptor kinase 1 202716_at 7.60 2.50 3.05 + PTPN1 protein tyrosine phosphatase, non-receptor type 1 215984_s_at 129.29 44.77 2.89 + ARFRP1 ADP-ribosylation factor related protein 1 219837_s_at 84.68 29.97 2.83 − CYTL1 cytokine-like 1 207987_s_at 96.20 34.37 2.80 − GNRH1 gonadotropin-releasing hormone 1 204115_at 15.78 5.64 2.80 − GNG11 guanine nucleotide binding protein (G protein), gamma 11 218157_x_at 13.07 4.70 2.78 + CDC42SE1 CDC42 small effector 1 211302_s_at 34.25 12.62 2.71 + PDE4B phosphodiesterase 4B, cAMP-specific 215904_at 40.46 15.15 2.67 + MLLT4 myeloid/lymphoid or mixed-lineage leukemia; translocated to, 4 205701_at 32.40 12.37 2.62 + IPO8 importin 8 202388_at 61.10 23.45 2.61 − RGS2 regulator of G-protein signalling 2, 24 kDa 213446_s_at 17.87 6.86 2.60 + IQGAP1 IQ motif containing GTPase activating protein 1 222201_s_at 23.74 9.21 2.58 − CASP8AP2 CASP8 associated protein 2 201065_s_at 8.99 3.55 2.53 + GTF2I general transcription factor II, I 35150_at 7.62 3.06 2.49 + CD40 CD40 antigen (TNF receptor superfamily member 5) 212294_at 10.32 4.16 2.48 − GNG12 guanine nucleotide binding protein (G protein), gamma 12 200644_at 9.85 4.00 2.46 + MARCKSL1 MARCKS-like 1 210221_at 14.37 5.85 2.46 + CHRNA3 cholinergic receptor, nicotinic, alpha polypeptide 3 211245_x_at 28.38 11.62 2.44 + KIR2DL4 killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 211242_x_at 78.57 32.17 2.44 + KIR2DL4 killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 4 221386_at 17.71 7.29 2.43 + OR3A2 olfactory receptor, family 3, subfamily A, member 2 202149_at 17.62 7.38 2.39 − NEDD9 neural precursor cell expressed, developmentally down-regulated 9 201008_s_at 50.83 21.32 2.38 + TXNIP thioredoxin interacting protein 202467_s_at 6.12 2.57 2.38 − COPS2 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis) 204396_s_at 14.32 6.12 2.34 − GRK5 G protein-coupled receptor kinase 5 396_f_at 9.39 4.05 2.32 + EPOR erythropoietin receptor 201488_x_at 2.09 0.91 2.31 + KHDRBS1 KH domain containing, RNA binding, signal transduction associated 1 221745_at 17.06 7.42 2.30 + WDR68 WD repeat domain 68 207667_s_at 15.45 6.73 2.30 + MAP2K3 mitogen-activated protein kinase kinase 3 209505_at 73.82 32.44 2.28 − NR2F1 Nuclear receptor subfamily 2, group F, member 1 213401_s_at 76.88 33.94 2.27 − — — 202091_at 16.37 7.23 2.26 + ARL2BP ADP-ribosylation factor-like 2 binding protein 201009_s_at 25.86 11.52 2.25 + TXNIP thioredoxin interacting protein 213270_at 5.27 2.36 2.24 + MPP2 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2) 209239_at 4.89 2.27 2.15 + NFKB1 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 211599_x_at 8.68 4.06 2.14 + MET met proto-oncogene (hepatocyte growth factor receptor) 205578_at 21.90 10.27 2.13 − ROR2 receptor tyrosine kinase-like orphan receptor 2 205176_s_at 5.32 2.50 2.13 − ITGB3BP integrin beta 3 binding protein (beta3- endonexin) 206132_at 1.84 0.87 2.11 + MCC mutated in colorectal cancers 203218_at 22.38 10.69 2.09 − MAPK9 mitogen-activated protein kinase 9 33814_at 10.79 5.17 2.09 + PAK4 p21(CDKN1A)-activated kinase 4 203077_s_at 5.06 2.43 2.08 − SMAD2 SMAD, mothers against DPP homolog 2 (Drosophila) 201431_s_at 9.40 4.52 2.08 − DPYSL3 dihydropyrimidinase-like 3 221060_s_at 14.80 7.12 2.08 + TLR4 toll-like receptor 4 204712_at 58.79 28.53 2.06 − WIF1 WNT inhibitory factor 1 200923_at 21.83 10.68 2.04 + LGALS3BP lectin, galactoside-binding, soluble, 3 binding protein 204064_at 8.66 4.25 2.04 − THOC1 THO complex 1 218158_s_at 8.68 4.29 2.02 − APPL adaptor protein containing pH domain, PTB domain and leucine zipper motif 1 204813_at 7.04 3.50 2.01 + MAPK10 mitogen-activated protein kinase 10 208486_at 3.82 1.91 2.00 + DRD5 dopamine receptor D5 Cation transport 205802_at 76.09 17.70 4.30 − TRPC1 transient receptor potential cation channel, subfamily C, member 1 203688_at 16.25 4.21 3.86 − PKD2 polycystic kidney disease 2 (autosomal dominant) 205803_s_at 21.92 6.71 3.26 − TRPC1 transient receptor potential cation channel, subfamily C, member 1 212297_at 4.78 1.92 2.49 − ATP13A3 ATPase type 13A3 208349_at 5.70 2.33 2.45 + TRPA1 transient receptor potential cation channel, subfamily A, member 1 Calcium ion transport 205802_at 60.75 14.13 4.30 − TRPC1 transient receptor potential cation channel, subfamily C, member 1 205803_s_at 17.50 5.36 3.26 − TRPC1 transient receptor potential cation channel, subfamily C, member 1 219090_at 32.29 13.55 2.38 − SLC24A3 solute carrier family 24 (sodium/potassium/calcium exchanger), member 3 Protein modification 220483_s_at 131.49 33.34 3.94 + RNF19 ring finger protein 19 205571_at 16.80 4.32 3.89 − LIPT1 lipoyltransferase 1 208689_s_at 13.18 4.81 2.74 + RPN2 ribophorin II 213704_at 12.56 5.11 2.46 − RABGGTB Rab geranylgeranyltransferase, beta subunit Intracellular signaling cascade 209648_x_at 35.05 8.74 4.01 − SOCS5 suppressor of cytokine signaling 5 208127_s_at 21.05 5.61 3.75 − SOCS5 suppressor of cytokine signaling 5 219165_at 14.50 4.12 3.52 − PDLIM2 PDZ and LIM domain 2 (mystique) 212729_at 13.42 3.94 3.41 + DLG3 discs, large homolog 3 (neuroendocrine-dlg, Drosophila) 221748_s_at 17.17 5.23 3.28 − TNS1 tensin 1 215829_at 13.31 4.23 3.15 + SHANK2 SH3 and multiple ankyrin repeat domains 2 209895_at 68.09 22.31 3.05 + PTPN11 protein tyrosine phosphatase, non-receptor type 11 212801_at 5.40 1.77 3.04 + CIT citron (rho-interacting, serine/threonine kinase 21) 202226_s_at 55.90 18.78 2.98 + CRK v-crk sarcoma virus CT10 oncogene homolog (avian) 213337_s_at 11.05 3.83 2.88 + SOCS1 suppressor of cytokine signaling 1 209684_at 5.91 2.06 2.87 − RIN2 Ras and Rab interactor 2 207732_s_at 17.40 6.20 2.81 + DLG3 discs, large homolog 3 (neuroendocrine-dlg, Drosophila) 203370_s_at 30.18 11.04 2.73 − PDLIM7 PDZ and LIM domain 7 (enigma) 213545_x_at 12.62 4.65 2.71 − SNX3 sorting nexin 3 205880_at 6.88 2.57 2.68 − PRKD1 protein kinase D1 210648_x_at 10.35 3.91 2.65 − SNX3 sorting nexin 3 202114_at 10.97 4.15 2.64 − SNX2 sorting nexin 2 218705_s_at 22.90 8.73 2.62 − SNX24 sorting nexing 24 220300_at 24.59 9.42 2.61 − RGS3 regulator of G-protein signalling 3 205147_x_at 5.11 2.01 2.54 + NCF4 neutrophil cytosolic factor 4, 40 kDa 207782_s_at 25.02 9.94 2.52 + PSEN1 presenilin 1 200604_s_at 23.18 9.21 2.52 + PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha 200067_x_at 7.46 3.22 2.32 − SNX3 sorting nexin 3 207105_s_at 5.09 2.20 2.32 + PIK3R2 phosphoinositide-3-kinase, regulatory subunit 2 (p85 beta) 205170_at 9.41 4.22 2.23 + STAT2 signal transducer and activator of transcription 2, 113 kDa 215411_s_at 23.50 10.69 2.20 − TRAF3IP2 TRAF3 interacting protein 2 219457_s_at 15.25 7.45 2.05 − RIN3 Ras and Rab interactor 3 221526_x_at 12.87 6.32 2.04 + PARD3 par-3 partitioning defective 3 homolog (C. elegans) 209154_at 3.29 1.66 1.98 − TAX1BP3 Tax1 binding protein 3 202987_at 19.16 9.79 1.96 − TRAF3IP2 TRAF3 interacting protein 2 mRNA processing 222040_at 36.12 11.14 3.24 − HNRPA1 heterogeneous nuclear ribonucleoprotein A1 208765_s_at 21.68 6.81 3.18 + HNRPR heterogeneous nuclear ribonucleoprotein R 221919_at 28.33 9.18 3.09 − — — 205063_at 23.40 7.98 2.93 − SIP1 survival of motor neuron protein interacting protein 1 201488_x_at 2.29 0.99 2.31 + KHDRBS1 KH domain containing, RNA binding, signal transduction associated 1 201224_s_at 10.50 4.62 2.27 + SRRM1 serine/arginine repetitive matrix 1 RNA splicing 200686_s_at 20.70 5.73 3.61 − SFRS11 splicing factor, arginine/serine-rich 11 203376_at 7.85 2.56 3.06 − CDC40 cell division cycle 40 homolog (yeast) 209162_s_at 45.56 16.91 2.69 + PRPF4 PRP4 pre-mRNA processing factor 4 homolog (yeast) 200685_at 17.66 7.35 2.40 − SFRS11 splicing factor, arginine/serine-rich 11 201362_at 9.18 4.04 2.27 − IVNS1ABP influenza virus NS1A binding protein 202127_at 10.12 4.53 2.23 − PRPF4B PRP4 pre-mRNA processing factor 4 homolog B (yeast) 221546_at 31.65 14.76 2.14 + PRPF18 PRP18 pre-mRNA processing factor 18 homolog (yeast) 214016_s_at 8.05 4.02 2.00 − SFPQ Splicing factor proline/glutamine-rich Endotosis 209839_at 37.68 6.99 5.39 − DNM3 dynamin 3 209684_at 3.32 1.16 2.87 − RIN2 Ras and Rab interactor 2 213545_x_at 7.08 2.61 2.71 − SNX3 sorting nexin 3 210648_x_at 5.81 2.20 2.65 − SNX3 sorting nexin 3 202114_at 6.16 2.33 2.64 − SNX2 sorting nexin 2 200067_x_at 4.19 1.81 2.32 − SNX3 sorting nexin 3 207287_at 7.81 3.74 2.09 − FLJ14107 hypothetical protein FLJ14107 219457_s_at 8.56 4.18 2.05 − RIN3 Ras and Rab interactor 3 Regulation of transcription from PolII promoter 219778_at 58.94 14.41 4.09 − ZFPM2 zinc finger protein, multitype 2 221773_at 13.43 3.93 3.42 − ELK3 ELK3, ETS-domain protein (SRF accessory protein 2) 211251_x_at 11.18 3.69 3.03 + NFYC nuclear transcription factor Y, gamma 202724_s_at 9.60 3.34 2.88 − FOXO1A forkhead box O1A 212257_s_at 14.37 5.13 2.80 + SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 202216_x_at 9.15 3.28 2.79 + NFYC nuclear transcription factor Y, gamma 204349_at 9.97 3.90 2.56 − CRSP9 cofactor required for Sp1 transcriptional activation, subunit 9, 33 kDa 200604_s_at 18.43 7.33 2.52 + PRKAR1A protein kinase, cAMP-dependent, regulatory, type I, alpha 206858_s_at 13.06 5.74 2.28 − HOXC6 homeo box C6 205170_at 7.49 3.35 2.23 + STAT2 signal transducer and activator of transcription 2, 113 kDa 213891_s_at 11.07 4.97 2.23 − TCF4 Transcription factor 4 201073_s_at 9.51 4.49 2.12 + SMARCC1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 213251_at 2.17 1.07 2.03 − SMARCA5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 209292_at 21.21 10.46 2.03 − ID4 Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein 209189_at 61.47 30.61 2.01 − FOS v-fos FBJ murine osteosarcoma viral oncogene homolog 202172_at 6.04 3.07 1.97 − ZNF161 zinc finger protein 161 Regulation of cell cycle 216061_x_at 7.05 2.09 3.38 − PDGFB platelet-derived growth factor beta polypeptide 209550_at 23.27 7.33 3.18 − NDN necdin homolog (mouse) 214683_s_at 30.04 9.83 3.05 − CLK1 CDC-like kinase 1 211251_x_at 11.58 3.82 3.03 + NFYC nuclear transcription factor Y, gamma 202216_x_at 9.48 3.40 2.79 + NFYC nuclear transcription factor Y, gamma 205106_at 47.82 17.22 2.78 + MTCP1 mature T-cell proliferation 1 219910_at 4.96 1.83 2.71 + HYPE Huntingtin interacting protein E 207239_s_at 17.48 7.09 2.47 + PCTK1 PCTAIRE protein kinase 1 202149_at 15.25 6.39 2.39 − NEDD9 neural precursor cell expressed, developmentally down-regulated 9 38707_r_at 1.72 0.80 2.16 + E2F4 E2F transcription factor 4, p107/p130-binding 204566_at 6.86 3.21 2.14 − PPM1D protein phosphatase 1D magnesium- dependent, delta isoform 201700_at 5.14 2.44 2.11 + CCND3 cyclin D3 200712_s_at 5.65 2.72 2.07 + MAPRE1 microtubule-associated protein, RP/EB family, member 1 206272_at 3.58 1.78 2.02 − SPHAR S-phase response (cyclin-related) 208824_x_at 11.71 5.83 2.01 + PCTK1 PCTAIRE protein kinase 1 2028_s_at 1.07 0.55 1.95 + E2F1 E2F transcription factor 1 Protein complex assembly 212511_at 7.99 2.34 3.41 − PICALM phosphatidylinositol binding clathrin assembly protein 216711_s_at 10.27 3.05 3.37 + TAF1 TATA box binding protein (TBP)-associated factor 200771_at 9.13 3.21 2.84 − LAMC1 laminin, gamma 1 (formerly LAMB2) 201624_at 11.70 4.68 2.50 − DARS aspartyl-tRNA synthetase 35150_at 5.91 2.37 2.49 + CD40 CD40 antigen (TNF receptor superfamily member 5) 213480_at 2.70 1.11 2.44 − VAMP4 vesicle-associated membrane protein 4 213270_at 4.09 1.83 2.24 + MPP2 membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2) 208829_at 8.14 3.73 2.18 + TAPBP TAP binding protein (tapasin) 216125_s_at 13.70 6.39 2.15 + RANBP9 RAN binding protein 9 212128_s_at 12.43 5.88 2.11 + DAG1 dystroglycan 1 (dystrophin-associated glycoprotein 1) 200841_s_at 41.38 20.07 2.06 + EPRS glutamyl-prolyl-tRNA synthetase 221526_x_at 9.49 4.67 2.04 + PARD3 par-3 partitioning defective 3 homolog (C. elegans) Protein biosynthesis 218830_at 23.85 6.25 3.82 − RPL26L1 ribosomal protein L26-like 1 202247_s_at 24.00 6.89 3.48 + MTA1 metastasis associated 1 214317_x_at 21.82 7.39 2.95 − RPS9 Ribosomal protein S9 200026_at 5.33 1.91 2.78 − RPL34 ribosomal protein L34 200963_x_at 4.64 1.76 2.63 − RPL31 ribosomal protein L31 221693_s_at 25.44 9.85 2.58 + MRPS18A mitochondrial ribosomal protein S18A 219762_s_at 15.45 6.27 2.46 − RPL36 ribosomal protein L36 221593_s_at 22.43 9.34 2.40 − RPL31 ribosomal protein L31 200091_s_at 3.20 1.36 2.35 − RPS25 ribosomal protein S25 208756_at 9.21 4.09 2.25 + EIF3S2 eukaryotic translation initiation factor 3, subunit 2 beta, 36 kDa 203781_at 9.61 4.31 2.23 − MRPL33 mitochondrial ribosomal protein L33 202926_at 9.86 4.58 2.15 + NAG neuroblastoma-amplified protein 213687_s_at 6.78 3.19 2.13 − RPL35A ribosomal protein L35a 212450_at 11.03 5.32 2.07 − KIAA0256 KIAA0256 gene product 214143_x_at 4.08 2.08 1.96 − RPL24 ribosomal protein L24 Cell cycle 216711_s_at 14.05 4.17 3.37 + TAF1 TATA box binding protein (TBP)-associated factor 215747_s_at 17.66 5.57 3.17 + RCC1 regulator of chromosome condensation 1 203531_at 4.39 1.56 2.81 − CUL5 cullin 5 213743_at 11.99 4.29 2.79 − CCNT2 cyclin T2 217301_x_at 21.86 8.16 2.68 + RBBP4 retinoblastoma binding protein 4 202388_at 64.82 24.87 2.61 − RGS2 regulator of G-protein signalling 2, 24 kDa 209903_s_at 10.39 4.17 2.49 − ATR ataxia telangiectasia and Rad3 related 205245_at 8.76 3.79 2.32 + PARD6A par-6 partitioning defective 6 homolog alpha (C. elegans) 213151_s_at 2.56 1.13 2.27 − 38967 septin 7 212332_at 63.97 29.53 2.17 + RBL2 retinoblastoma-like 2 (p130) 205895_s_at 6.88 3.26 2.11 + NOLC1 nucleolar and coiled-body phosphoprotein 1 206967_at 19.89 9.81 2.03 + CCNT1 cyclin T1

In ER-negative tumors, examples of pathways with genes that had both positive or negative correlation to DMFS include Regulation of cell growth (FIG. 2 b), the most significant pathway (Table 2), and Cell adhesion (FIG. 2 d). Of the top 20 pathways in ER-negative tumors, none showed a dominant positive association with DMFS, but some did display a dominant negative correlation (FIG. 6 online) including Regulation of G-protein coupled receptor signaling (FIG. 2 f), Skeletal development (FIG. 2 h), and the pathways ranked among the top 3 in significance (Table 2). Of the top 20 core pathways 4 overlapped between ER-positive and -negative tumors, i.e., Regulation of cell cycle, Protein amino acid phosphorylation, Protein biosynthesis, and Cell cycle (Table 2).

In an attempt to use gene expression profiles in the most significant biological processes to predict distant metastases we used the genes of the top 2 significant pathways in both ER-positive and -negative tumors (Table 7) to construct a gene signature for prediction of distant recurrence. A 50-gene signature was constructed by combining the 38 genes from the top 2 ER-positive pathways and 12 genes for the top 2 ER-negative pathways. The Affymetrix U133A data on a recently published set of breast tumors with follow-up information²¹ was used as an independent test set to validate the signature. The 152-patient validation set consisted of 125 ER-positive tumors and 27 ER-negative tumors. When the 38-gene signature was applied to ER-positive tumors, an ROC analysis gave an AUC of 0.782 (FIG. 3 a), and Kaplan-Meier analysis for DMFS showed a clear separation in risk groups

Probe Set SD* z-Score DMFS† Gene Symbol Gene Title 208905_at 3.04 4.29 − CYCS cytochrome c, somatic 204817_at 9.77 3.73 − ESPL1 extra spindle poles like 1 38158_at 7.23 3.41 − ESPL1 extra spindle poles like 1 204947_at 16.65 3.04 − E2F1 E2F transcription factor 1 201111_at 6.18 3.04 − CSE1L CSE1 chromosome segregation 1-like 201636_at 2.34 2.97 − FXR1 fragile X mental retardation, autosomal homolog 1 220048_at 1.28 2.82 − EDAR ectodysplasin A receptor 210766_s_at 4.54 2.75 − CSE1L CSE1 chromosome segregation 1-like 221567_at 6.81 2.66 − NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) 213829_x_at 2.54 2.65 − TNFRSF6B tumor necrosis factor receptor superfamily, member 6b, decoy 201112_s_at 2.79 2.57 − CSE1L CSE1 chromosome segregation 1-like 212353_at 10.77 2.51 − SULF1 sulfatase 1 208822_s_at 1.81 2.47 − DAP3 death associated protein 3 209462_at 36.92 2.37 − APLP1 amyloid beta (A4) precursor-like protein 1 203005_at 1.98 2.29 − LTBR lymphotoxin beta receptor (TNFR superfamily, member 3) 202731_at 11.50 4.01 + PDCD4 programmed cell death 4 206150_at 18.92 3.57 + TNFRSF7 tumor necrosis factor receptor superfamily, member 7 202730_s_at 8.73 3.18 + PDCD4 programmed cell death 4 209539_at 9.89 3.14 + ARHGEF6 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 212593_s_at 12.82 3.07 + PDCD4 programmed cell death 4 204933_s_at 45.18 2.96 + TNFRSF11B tumor necrosis factor receptor superfamily, member 11b 209831_x_at 2.59 2.43 + DNASF2 deoxyribonuclease II, lysosomal 203187_at 3.21 2.38 + DOCK1 dedicator of cytokinesis 1 210164_at 23.24 2.34 + GZMB granzyme B (HR=3.36) (FIG. 3 b). For the 12-gene signature for ER-negative tumors, an AUC of 0.872 (FIG. 3 c) and a HR of 19.8 (FIG. 3 d) were obtained. The combined 50-gene signature for ER-positive and ER-negative tumors gave an AUC of 0.795 (FIG. 3 e) and a HR of 4.44 (FIG. 3 f). Thus a gene signature can now be derived by combining statistical methods and biological knowledge. The present invention provides not only a new way to derive gene signatures for cancer prognosis, but also an insight to the distinct biological processes between subgroups of tumors.

TABLE 7 Genes used for prediction in top pathways Significant genes in the Apoptosis pathways in ER-positive tumors Significant genes in the Regulation of cell cycle pathway in ER-positive tumors Probe Set SD* z-Score DMFS† Gene Symbol Gene Title Significant genes in the Regulation of cell growth pathway in ER-negative tumors 204817_at 8.90 3.73 − ESPL1 extra spindle poles like 1 (S. cerevisiae) 38158_at 6.60 3.41 − ESPL1 extra spindle poles like 1 (S. cerevisiae) 214710_s_at 7.19 3.10 − CCNB1 cyclin B1 212426_s_at 2.55 3.08 − YWHAQ tyrosine 3-/tryptophan 5-monooxygenase activation protein 204009_s_at 2.53 3.08 − KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog 204947_at 15.18 3.04 − E2F1 E2F transcription factor 1 201947_s_at 2.30 3.04 − CCT2 chaperonin containing TCP1, subunit 2 (beta) 204822_at 14.49 2.91 − TTK TTK protein kinase 209096_at 2.77 2.57 − UBE2V2 ubiquitin-conjugating enzyme E2 variant 2 204826_at 4.33 2.53 − CCNF cyclin F 212022_s_at 14.44 2.46 − MKI67 antigen identified by monoclonal antibody Ki-67 202647_s_at 3.41 2.42 − NRAS neuroblastoma RAS viral (v-ras) oncogene homolog 201076_at 2.43 3.09 + NHP2L1 NHP2 non-histone chromosome protein 2-like 1 (S. cerevisiae) 201601_x_at 8.16 3.00 + IFITM1 interferon induced transmembrane protein 1 (9-27) 204015_s_at 24.75 2.90 + DUSP4 dual specificity phosphatase 4 220407_s_at 6.36 2.68 + TGFB2 transforming growth factor, beta 2 206404_at 10.98 2.38 + FGF9 fibroblast growth factor 9 (glia-activating factor) 209648_x_at 5.77 4.01 − SOC55 suppressor of cytokine signaling 5 208127_s_at 3.71 3.75 − SOC55 suppressor of cytokine signaling 5 209550_at 5.88 3.18 − NDN necdin homolog (mouse) 201162_at 5.15 3.14 − IGFBP7 insulin-like growth factor binding protein 7 213910_at 12.99 2.87 − IGFBP7 insulin-like growth factor binding protein 7 212279_at 4.53 2.91 + MAC30 hypothetical protein MAC30 213337_s_at 2.53 2.88 + SOCS1 suppressor of cytokine signaling 1 Significant genes in the Regulation of G-protein coupled receptor signaling pathway in ER-negative tumors 204337_at 7.89 3.99 − RGS4 regulator of G-protein signalling 4 209324_s_at 2.73 3.73 − RGS16 regulator of G-protein signalling 16 220300_at 3.61 2.61 − RGS3 regulator of G-protein signalling 3 202388_at 9.45 2.61 − RGS2 regulator of G-protein signalling 2, 24 kDa 204396_s_at 2.47 2.34 − GRK5 G protein-coupled receptor kinase 5 *SD = Standard deviation †DMFS = distant metastasis-free survival; + = positive correlation with DMFS, − = negative correlation with DMFS

To compare genes from various prognostic signatures for breast cancer, five published gene signatures were selected^(6,8,21-23). We first compared the gene sequence identity between each pair of the gene signatures and found very few overlapping genes as expected (Table 8). The gene expression grade index comprising 97 genes, of which most are associated with cell cycle regulation and proliferation²¹, showed the highest number of overlapping genes between the various signatures ranging from 5 with the 16 genes of Genomic Health²² to 10 with Yu's 62 genes²³. The other 4 gene signatures showed only 1 gene overlap in pair-wise comparison, and there was no common gene for all signatures. In spite of the low number of overlapping genes across signatures, which are due to different platforms and bioinformatical analyses used and different groups of patients analyzed, we found that the representation of common pathways in the various signatures may underlie their individual prognostic value⁸. Therefore, we examined the representation of the top 20 core pathways (Table 2) in the 5 signatures, the genes in the signatures were mapped to GOBP. Except the Genomic Health 16-gene signature mapped to 10 distinct core pathways, each of the other 4 signatures with 62 genes or more mapped to 19 distinct core prognostic pathways (Table 3). Of these 19 pathways, 8 were identical for all 4 signatures, i.e., Mitosis, Apoptosis, Regulation of cell cycle, DNA repair, Cell cycle, Protein amino acid phosphorylation, Intracellular signaling cascade, and Cell adhesion. The other 11 pathways were either present in 1, 2, or 3, of the signatures, but not in all (Table 3). In a recent study, comparing the prognostic performance of different gene signatures, agreement in outcome predictions were found as well²⁴. However, in contrast to our present approach, the underlying pathways were not investigated, and merely the performance of various gene signatures on a single patient cohort, heterogeneous with respect to nodal status and adjuvant systemic therapy²⁵, was compared²⁴. It is important to note, however, that although similar pathways are represented in various signatures, it does not necessarily mean the individual genes in a pathway contribute equally and into the same direction. Genes in a specific pathway may be positively or negatively associated with tumor aggressiveness, and have very different contributions and significance levels (FIGS. 5 and 6, and Tables 5 and 6).

TABLE 8 Number of common genes between different gene signatures for breast cancer prognosis Genomic Wang's 76 van't Veer's 70 Health 16 genes genes genes Yu's 62 genes Wang's 76 CCNE2 No genes No genes genes* van 't Veer's CNNE2 SCUBE2 AA962149 70 genes† Genomic No genes SCUBE2 BIRC5 Health 16 genes‡ Yu's 62 genes* No genes AA962149 BIRC5 Sotiriou's 97 PLK1, FEN1, MELK, MYBL2, URCC6, FOXM1, genes* CCNE2, CENPA, BIRC5, STK6, DLG7, GTSE1, CCNE2, MKI67, DKFZp686L20222, KPNA2, GMPS, DC13, CCNB1 DC13, FLJ32241, MLF1IP, PRC1, HSP1CDC21, CDC2, POLQ NUSAP1, KIF11, EXO1 KNTC2 *Affymetrix HG-U133A Genechip †Agilent Hu25K microarray ‡No genome-wide assessment; RT-PCR

TABLE 3 Mapping various gene signatures to core pathways Published gene signatures^(a) Pathways GO_ID Wang Van 't Veer Paik Yu Sotiriou ER-positive tumors Apoptosis 6915 X X X X X Regulation of cell cycle 74 X X X X X Protein amino acid phosphorylation 6468 X X X X X Cytokinesis 910 X X X X Cell motility 6928 X X Cell cycle 7049 X X X X X Cell surface receptor-linked signal transduction 7166 X Mitosis 7067 X X X X X Intracellular protein transport 6886 X X X Mitotic chromosome segregation 70 X X X Ubiquitin-dependent protein catabolism 6511 X X X DNA repair 6281 X X X X Induction of apoptosis 6917 X Immune response 6955 X X X Protein biosynthesis 6412 X X X DNA replication 6260 X X X X Oncogenesis 7048 X X X Metabolism 8152 X X Cellular defense response 6968 X X X Chemotaxis 6935 X X ER-negative tumors Regulation of cell growth 1558 X Regulation of G-coupled receptor signaling 8277 Skeletal development 1501 X X Protein amino acid phosphorylation 6468 X X X X X Cell adhesion 7155 X X X X Carbohydrate metabolism 5975 X X Nuclear mRNA splicing, via spliceosome 398 Signal transduction 7165 X X X X Cation transport 6812 Calciumion transport 6816 Protein modification 6464 Intracellular signaling cascade 7242 X X X X mRNA processing 6397 RNA splicing 8380 Endocytosis 6897 Regulation of transcription from PolII promoter 6357 X Regulation of cell cycle 74 X X X Protein complex assembly 6461 X X Protein biosynthesis 6412 X X Cell cycle 7049 X X X X X ^(a)Published gene signatures that were studied include the 76-gene signature by Wang et al⁸, the 70-gene signature by van 't Veer et al⁶, the 16-gene signature by Paik et al²², the 62-gene signature by Yu et al²³, and the 97-gene signature by Sotiriou et al²¹. Individual genes in each signature were mapped to the top 20 core pathways for ER-positive and ER-negative tumors.

In conclusion, we have shown that gene signatures can be derived by combining statistical methods and biological knowledge. Our study for the first time applied a method that systematically evaluated the biological pathways related to patient outcomes of breast cancer and have provided biological evidence that various published prognostic gene signatures providing similar outcome predictions are based on the representation of common biological processes. Identification of the key biological processes, rather than the assessment of signatures based on individual genes, provides targets for future drug development.

The following examples are provided to illustrate but not limit the claimed invention. All references cited herein are hereby incorporated herein by reference.

EXAMPLE 1 Methods

Patient population. The study was approved by the Medical Ethics Committee of the Erasmus MC Rotterdam, The Netherlands (MEC 02.953), and was performed in accordance to the Code of Conduct of the Federation of Medical Scientific Societies in the Netherlands (www.fmwv.nl). A cohort of 344 breast tumor samples from a tumor bank at the Erasmus Medical Center (Rotterdam, Netherlands) were used in this study. All these samples were from patients with lymph node-negative breast cancer who had not received any adjuvant systemic therapy, and had more than 70% tumor content. Among them, 286 samples had been used to derive a 76-gene signature to predict distant metastasis⁸. An additional 58 ER-negative cases were included to increase the numbers in this subgroup in the analyses performed. In this study, ER status for a patient was determined based on the expression level of the ER gene on the chip. A patient is considered ER-positive if its ER expression level is higher than 1000 after scaling the average of intensity on a chip to 600. Otherwise, the patient is ER-negative²⁶. As a result, there were 221 ER-positive and 123 ER-negative patients in the 344-patient population. The mean age of the patients was 53 years (median 52, range 26-83 years), 175 (51%) were premenopausal and 169 (49%) postmenopausal. T1 tumors (≦2 cm) were present 168 patients (49%), T2 tumors (>2-5 cm) in 163 patients (47%), T3/4 tumors (>5 cm) in 12 patients (3%), and 1 patient with unknown tumor stage. Pathological examination was carried out by regional pathologists as described previously²⁷ and the histological grade was coded as poor in 184 patients (54%), moderate in 45 patients (13%, good in 7 patients (2%), and unknown for 108 patients (31%). During follow-up 103 patients showed a relapse within 5 years and were counted as failures in the analysis for DMFS. Eighty two patients died after a previous relapse. The median follow-up time of patients still alive was 101 months (range 61-171 months).

RNA isolation and hybridization. Total RNA was extracted from 20-40 cryostat sections of 30 um thickness with RNAzol B (Campro Scientific, Veenendaal, Netherlands). After being biotinylated, targets were hybridized to Affymetrix HG-U133A chips as described⁸. Gene expression signals were calculated using Affymetrix GeneChip analysis software MAS 5.0. Chips with an average intensity less than 40 or a background higher than 100 were removed. Global scaling was performed to bring the average signal intensity of a chip to a target of 600 before data analysis.

For the validation dataset²¹, quantile normalization was performed and ANOVA was used to eliminate batch effects from different sample preparation methods, RNA extraction methods, different hybridization protocols and scanners.

Multiple gene signatures. Since gene expression patterns of ER-positive breast tumors are quite different from that of ER-negative breast tumors⁸, data analysis to derive gene signatures and subsequent pathway analysis were conducted separately. For either ER-positive or ER-negative patients, 80 samples were randomly selected as a training set. For the training set, univariant Cox proportional-hazards regression was performed to identify genes whose expression patterns were most correlated to patients' distant metastasis-free survival (DMFS) time. Our previous analysis suggested that 80 patients represent a minimum size of the training set for producing a prognostic gene signature of stable performance⁸. The top 100 genes were used as a signature to predict tumor recurrence for the remaining independent patients as a test set. A receiver operating characteristic (ROC) analysis with distant metastasis within 5 years as a defining point was conducted. The area under curve (AUC) was used as a measurement of the performance of a signature in the test set. The above procedure was repeated 500 times (FIG. 4). Thus, 500 signatures of 100 genes each were obtained. The frequency of the selected genes in the 500 signatures was calculated and the genes were ranked based on the frequency.

As a control, the patient clinical information for the ER-positive patients or ER-negative patients was permutated randomly and reassigned to the chip data. As described above, 80 chips were then randomly selected as a training set and the top 100 genes were selected using the Cox modeling based on the permutated clinical information. The top 100 genes were then used as a signature to predict relapse in the remaining patients. The clinical information was permutated 10 times. For each permutation of the clinical information, 50 various training sets of 80 patients were created. For each training set, the top 100 genes were obtained as a control gene list based on the Cox modeling. Thus, a total of 500 control signatures were obtained. The predictive performance of the 100 genes was examined in the remaining patients. An ROC analysis was conducted and AUC was calculated in the test set.

Mapping to GOBP. To identify over-representation of biological pathways in the signatures, genes on Affymetrix HG-U133A chip were mapped to the categories of GOBP based on the annotation table downloaded from www.affymetrix.com. Categories that contain at least 10 probe sets from HG-U133A chip were retained for subsequent pathway analysis. The 100 genes of each signature were mapped to GOBP. Hypergeometric distribution probabilities for GOBP categories were calculated for each signature. A pathway that has a hypergeometric distribution probability <0.05 and was hit by two or more genes from the 100 genes was considered as an over-represented pathway in a signature. The total number of a pathway appeared in the 500 signatures was considered as the frequency of over-representation.

Global Test program. To evaluate the relationship between a pathway and the clinical outcome, each of the top 20 over-represented pathways that have the highest frequencies in the 500 signatures were subjected to Global Test program^(1,2). The Global Test examines the association of a group of genes as a whole to a specific clinical parameter such as DMFS. The contribution of individual genes in the top over-represented pathways to the association was also evaluated and significant contributors were selected for subsequent analyses.

To explore the possibility of using the genes in a specific pathway as a signature to predict distant metastasis, the top two pathways for ER-positive or ER-negative tumors that were in the top 20 list based on frequency of over-representation and had the smallest P values from Global Test program were chosen to build a gene signature. First, genes in the pathway were selected if their z-score was greater than 1.95 from the Global Test program. A z-score greater than 1.95 indicates that the association of the gene expression with DMFS time is significant (P<0.05)^(1,2). The relapse score was the difference of weighted expression signals for negatively correlated genes and ones for positively correlated genes. To determine the optimal number of genes in a signature, ROC analysis was performed using signatures of various numbers of genes in the training set. The performance of the selected gene signature was evaluated by Kaplan-Meier survival analysis in an independent patient group²¹.

Comparing multiple gene signatures. To compare the genes from various prognostic signatures for breast cancer, five gene signatures were selected^(6,8,22-23). Identity of the genes between the signatures was determined by BLAST program. To examine the representation of the top 20 pathways in the signatures, genes in each of the signatures were mapped to GOBP.

Data Availability. The microarray data analyzed in this paper have been submitted to the NCBI/Genbank GEO database. The microarray and clinical data used for the independent validation testing set analysis were obtained from the Gene Expression Omnibus database (http://www.ncbi.nlm.hih.gov.geo) with accession code GSE2990.

Statistical Methods. Statistical analyses were conducted using the R system, version 2.2.1 (http://www.r-project.org). Cox proportional-hazard regression modeling analysis was performed to identify genes with a high correlation to DMFS in each training set. The survival package included in the R system was used for survival analysis. The hazard ratio (HR) and 95% confidence intervals (CI) were estimated using the stratified Cox regression analysis. Hypergeometric distribution probability analysis was performed to identify over-represented pathways in each of the 500 signatures. Global Test, version 3.1.1, was used to evaluate the top over-represented pathways related to DMFS and provided a way to visualize contributions of individual genes in a pathway.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, the descriptions and examples should not be construed as limiting the scope of the invention.

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Gene descriptions and SEQ ID NOS: SEQ ID NO: Accession Name Description PSID 1 KIAA0241 KIAA0241 protein 2 CD44 CD44 antigen (homing function and Indian blood group system) 3 ABCC5 ATP-binding cassette, sub-family C (CFTR/MRP), member 5 4 STK6 serine/threonine kinase 6 5 CYCS cytochrome c, somatic 6 KIA0406 KIAA0406 gene product 7 UCKL1 uridine-cytidine kinase 1-like 1 8 ZCCHC8 zinc finger, CCHC domain containing 8 9 RACGAP1 Rac GTPase activating protein 1 10 STAU staufen, RNA binding protein (Drosophila) 11 LACTB2 lactamase, beta 2 12 EEF1A2 eukaryotic translation elongation factor 1 alpha 2 13 RAE1 RAE1 RNA export 1 homolog (S. pombe) 14 TUFT1 tuftelin 1 15 ZFP36L2 zinc finger protein 36, C3H type-like 2 16 ORC6L origin recognition complex, subunit 6 homolog- like (yeast) 17 ZNF623 zinc finger protein 623 18 ESPL1 extra spindle poles like 1 19 TCEB1 transcription elongation factor B (SIII), polypeptide 1 20 RPS6KB1 ribosomal protein S6 kinase, 70 kDa, polypeptide 1 21 ZFPM2 zinc finger protein, multitype 2 22 RPL26L1 ribosomal protein L26-like 1 23 FLJ14346 hypothetical protein FLJ14346 24 MAPKAPK2 mitogen-activated protein kinase-activated protein kinase 2 25 COL2A1 collagen, type II, alpha 1 26 MBNL2 muscleblind-like 2 (Drosophila) 27 GPR124 G protein-coupled receptor 124 28 SFRS11 splicing factor, arginine/serine-rich 11 29 HNRPA1 heterogeneous nuclear ribonucleoprotein A1 30 CDC42BPA CDC42 binding protein kinase alpha (DMPK-like) 31 RGS4 regulator of G-protein signalling 4 32 TRPC1 transient receptor potential cation channel, subfamily C, member 1 33 TCF8 transcription factor 8 (represses interleukin 2 expression) 34 C6orf210 chromosome 6 open reading frame 210 35 DNM3 dynamin 3 36 Cep63 centrosome protein Cep63 37 TNFSF13 tumor necrosis factor (ligand) superfamily, member 13 38 DACT1 dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis) 39 RECK reversion-inducing-cysteine-rich protein with kazal motifs 40 CYCS cytochrome c, somatic 208905_at 41 PDCD4 programmed cell death 4 202731_at 42 ESPL1 extra spindle poles like 1 204817_at 43 TNFRSF7 tumor necrosis factor receptor superfamily, 206150_at member 7 44 ESPL1 extra spindle poles like 1 38158_at 45 PDCD4 programmed cell death 4 202730_s_at 46 ARHGEF6 Rac/Cdc42 guanine nucleotide exchange factor 209539_at (GEF) 6 47 PDCD4 programmed cell death 4 212593_s_at 48 E2F1 E2F transcription factor 1 204947_at 49 CSE1L CSE1 chromosome segregation 1-like 201111_at 50 FXR1 fragile X mental retardation, autosomal homolog 1 201636_at 51 TNFRSF11B tumor necrosis factor receptor superfamily, 204933_s_at member 11b 52 EDAR ectodysplasin A receptor 220048_at 53 CSE1L CSE1 chromosome segregation 1-like (yeast) 210766_s_at 54 NOL3 nucleolar protein 3 (apoptosis repressor with 221567_at CARD domain) 55 TNFRSF6B tumor necrosis factor receptor superfamily, 213829_x_at member 6b, decoy 56 CSE1L CSE1 chromosome segregation 1-like 201112_s_at 57 SULF1 sulfatase 1 212353_at 58 DAP3 death associated protein 3 208822_s_at 59 DNASE2 deoxyribonuclease II, lysosomal 209831_x_at 60 DOCK1 dedicator of cytokinesis 1 203187_at 61 APLP1 amyloid beta (A4) precursor-like protein 1 209462_at 62 GZMB granzyme B 210164_at 63 LTBR lymphotoxin beta receptor 203005_at 64 NFKB1 nuclear factor of kappa light polypeptide gene 209239_at enhancer in B-cells 1 (p105) 65 FADD Fas (TNFRSF6)-associated via death domain 202535_at 66 PHLDA2 pleckstrin homology-like domain, family A, 209803_s_at member 2 67 ELMO1 engulfment and cell motility 1 (ced-12 homolog, C. elegans) 204513_s_at 68 BIRC3 baculoviral IAP repeat-containing 3 210538_s_at 69 DDX41 DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 217840_at 70 IL17 interleukin 17 (cytotoxic T-lymphocyte-associated 208402_at serine esterase 8) 71 DNASE2 deoxyribonuclease II, lysosomal 214992_s_at 72 CXCR4 chemokine (C—X—C motif) receptor 4 209201_x_at 73 E2F1 E2F transcription factor 1 2028_s_at 74 TXNL1 thioredoxin-like 1 201588_at 75 MAP3K5 mitogen-activated protein kinase kinase kinase 5 203836_s_at 76 FAS Fas (TNF receptor superfamily, member 6) 215719_x_at 77 CCNB1 cyclin B1 214710_s_at 78 NHP2L1 NHP2 non-histone chromosome protein 2-like 1 201076_at 79 YWHAQ tyrosine 3-monooxygenase/tryptophan 5- 212426_s_at monooxygenase activation protein 80 KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene 204009_s_at homolog 81 CCT2 chaperonin containing TCP1, subunit 2 (beta) 201947_s_at 82 IFITM1 interferon induced transmembrane protein 1 (9-27) 201601_x_at 83 TTK TTK protein kinase 204822_at 84 DUSP4 dual specificity phosphatase 4 204015_s_at 85 TGFB2 transforming growth factor, beta 2 220407_s_at 86 UBE2V2 ubiquitin-conjugating enzyme E2 variant 2 209096_at 87 CCNF cyclin F 204826_at 88 MKI67 antigen identified by monoclonal antibody Ki-67 212022_s_at 89 NRAS neuroblastoma RAS viral (v-ras) oncogene 202647_s_at homolog 90 FGF9 fibroblast growth factor 9 (glia-activating factor) 206404_at 91 CCNB2 cyclin B2 202705_at 92 CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) 202870_s_at 93 JAK2 Janus kinase 2 (a protein tyrosine kinase) 205842_s_at 94 IFITM1 interferon induced transmembrane protein 1 (9-27) 214022_s_at 95 NFYC nuclear transcription factor Y, gamma 211251_x_at 96 DUSP4 dual specificity phosphatase 4 204014_at 97 RBBP6 retinoblastoma binding protein 6 212781_at 98 STK6 serine/threonine kinase 6 208079_s_at 99 STK6 serine/threonine kinase 6 204092_s_at 100 NEK2 NIMA (never in mitosis gene a)-related kinase 2 204641_at 101 LYN v-yes-1 Yamaguchi sarcoma viral related 210754_s_at oncogene homolog 102 RPS6KC1 ribosomal protein S6 kinase, 52 kDa, polypeptide 1 218909_at 103 GMFB glia maturation factor, beta 202543_s_at 104 MELK maternal embryonic leucine zipper kinase 204825_at 105 CDC2 Cell division cycle 2, G1 to S and G2 to M 203213_at 106 RPS6KB1 ribosomal protein S6 kinase, 70 kDa, polypeptide 1 204171_at 107 PRKCH protein kinase C, eta 218764_at 108 CCL2 chemokine (C-C motif) ligand 2 216598_s_at 109 BUB1B BUB1 budding uninhibited by benzimidazoles 1 203755_at homolog beta (yeast) 110 TGFBR2 transforming growth factor, beta receptor II 208944_at (70/80 kDa) 111 SGK3 serum/glucocorticoid regulated kinase family, 220038_at member 3 112 BUB1 BUB1 budding uninhibited by benzimidazoles 1 209642_at homolog (yeast) 113 ATP6AP1 ATPase, H+ transporting, lysosomal accessory 207957_s_at protein 1 114 HCK hemopoietic cell kinase 208018_s_at 115 FYN FYN oncogene related to SRC, FGR, YES 212486_s_at 116 FYN FYN oncogene related to SRC, FGR, YES 216033_s_at 117 LATS1 LATS, large tumor suppressor, homolog 1 219813_at (Drosophila) 118 NUAK2 NUAK family, SNF1-like kinase, 2 220987_s_at 119 NEK7 NIMA (never in mitosis gene a)-related kinase 7 212530_at 120 PRKD2 protein kinase D2 209282_at 121 SRPK1 SFRS protein kinase 1 202200_s_at 122 PRC1 protein regulator of cytokinesis 1 218009_s_at 123 CENPE centromere protein E, 312 kDa 205046_at 124 SMC1L1 SMC1 structural maintenance of chromosomes 1- 201589_at like 1 125 PAFAH1B1 platelet-activating factor acetylhydrolase, isoform 200815_s_at lb, alpha subunit 45 kDa 126 PPP1CC protein phosphatase 1, catalytic subunit, gamma 200726_at isoform 127 CKS1B CDC28 protein kinase regulatory subunit 1B 201897_s_at 128 CKS2 CDC28 protein kinase regulatory subunit 2 204170_s_at 129 CCNT2 cyclin T2 213743_at 130 HMMR hyaluronan-mediated motility receptor (RHAMM) 207165_at 131 CCR6 chemokine (C-C motif) receptor 6 206983_at 132 FN1 fibronectin 1 211719_x_at 133 IGF1 insulin-like growth factor 1 211577_s_at 134 FN1 fibronectin 1 210495_x_at 135 STAT3 signal transducer and activator of transcription 3 208991_at 136 TSPAN3 tetraspanin 3 200973_s_at 137 FN1 fibronectin 1 216442_x_at 138 IGF1 insulin-like growth factor 1 (somatomedin C) 209540_at 139 CORO1A coronin, actin binding protein, 1A 209083_at 140 IL8RB interleukin 8 receptor, beta 207008_at 141 STAT3 signal transducer and activator of transcription 3 208992_s_at 142 ACTR3 ARP3 actin-related protein 3 homolog (yeast) 213101_s_at 143 ARPC2 actin related protein 2/3 complex, subunit 2, 208679_s_at 34 kDa 144 SMC4L1 SMC4 structural maintenance of chromosomes 4- 201664_at like 1 145 SMC4L1 SMC4 structural maintenance of chromosomes 4- 215623_x_at like 1 146 HCAP-G chromosome condensation protein G 218663_at 147 MAD2L1 MAD2 mitotic arrest deficient-like 1 203362_s_at 148 JAG2 jagged 2 32137_at 149 STRN3 striatin, calmodulin binding protein 3 204496_at 150 HCAP-G chromosome condensation protein G 218662_s_at 151 SMC4L1 SMC4 structural maintenance of chromosomes 4- 201663_s_at like 1 152 RCC1 regulator of chromosome condensation 1 206499_s_at 153 CUL4B cullin 4B 202214_s_at 154 IL27RA interleukin 27 receptor, alpha 205926_at 155 PTPRC protein tyrosine phosphatase, receptor type, C 212587_s_at 156 IL6ST interleukin 6 signal transducer (gp130, oncostatin 211000_s_at M receptor) 157 KLRB1 killer cell lectin-like receptor subfamily B, member 1 214470_at 158 IL27RA interleukin 27 receptor, alpha 222062_at 159 CENPF centromere protein F, 350/400ka (mitosin) 209172_s_at 564 KIF2C kinesin family member 2C 209408_at 160 ERP29 endoplasmic reticulum protein 29 201216_at 161 AP2A2 adaptor-related protein complex 2, alpha 2 subunit 211779_x_at 162 AP2A2 adaptor-related protein complex 2, alpha 2 subunit 212159_x_at 163 KPNA2 karyopherin alpha 2 201088_at 164 RABIF RAB interacting factor 204478_s_at 165 ARF6 ADP-ribosylation factor 6 203311_s_at 166 COPA coatomer protein complex, subunit alpha 214337_at 167 RAB3A RAB3A, member RAS oncogene family 204974_at 168 APPBP2 amyloid beta precursor protein (cytoplasmic tail) 202630_at binding protein 2 169 RAB8A RAB8A, member RAS oncogene family 208819_at 170 VPS45A vacuolar protein sorting 45A 209268_at 171 VDP vesicle docking protein p115 201831_s_at 172 RAB22A RAB22A, member RAS oncogene family 218360_at 173 TMED1 transmembrane emp24 protein transport domain 203679_at containing 1 174 KIF20A kinesin family member 20A 218755_at 175 STX3A syntaxin 3A 209238_at 176 KDELR3 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum 204017_at protein retention receptor 3 177 NSF N-ethylmaleimide-sensitive factor 202395_at 178 RAB33B RAB33B, member RAS oncogene family 221014_s_at 179 SNX4 sorting nexin 4 212652_s_at 180 KPNA6 Karyopherin alpha 6 (importin alpha 7) 212103_at 181 RABIF RAB interacting factor 204477_at 182 ARF4 ADP-ribosylation factor 4 201097_s_at 183 TNPO1 Transportin 1 212635_at 184 STAM signal transducing adaptor molecule (SH3 domain 203544_s_at and ITAM motif) 1 185 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 211762_s_at 1) 186 CLTC clathrin, heavy polypeptide (Hc) 200614_at 187 RAB2 RAB2, member RAS oncogene family 208732_at 188 KDELR2 KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum 200699_at protein retention receptor 2 189 FBXO7 F-box protein 7 201178_at 190 PSMB4 proteasome (prosome, macropain) subunit, beta 202244_at type, 4 191 USP32 ubiquitin specific peptidase 32 211702_s_at 192 FBXW4 F-box and WD-40 domain protein 4 221519_at 193 SIAH1 seven in absentia homolog 1 (Drosophila) 202981_x_at 194 PSMB8 proteasome (prosome, macropain) subunit, beta 209040_s_at type, 8 195 PSMA6 proteasome (prosome, macropain) subunit, alpha 208805_at type, 6 196 PSMB4 proteasome (prosome, macropain) subunit, beta 202243_s_at type, 4 197 UBE2I Ubiquitin-conjugating enzyme E2I 208760_at 198 PSMA2 proteasome (prosome, macropain) subunit, alpha 201317_s_at type, 2 199 POLQ polymerase (DNA directed), theta 219510_at 200 RECQL4 RecQ protein-like 4 213520_at 201 NEIL3 nei endonuclease VIII-like 3 219502_at 202 RAD51AP1 RAD51 associated protein 1 204146_at 203 RAD54L RAD54-like 204558_at 204 BRCA1 breast cancer 1, early onset 204531_s_at 205 FANCL Fanconi anemia, complementation group L 218397_at 206 WSB2 WD repeat and SOCS box-containing 2 213734_at 207 HTATIP2 HIV-1 Tat interactive protein 2, 30 kDa 209448_at 208 IKBKG inhibitor of kappa light polypeptide gene enhancer 209929_s_at in B-cells, kinase gamma 209 LST1 leukocyte specific transcript 1 215633_x_at 210 LST1 leukocyte specific transcript 1 210629_x_at 211 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 204670_x_at 212 LST1 leukocyte specific transcript 1 211582_x_at 213 HLA-DRA major histocompatibility complex, class II, DR 210982_s_at alpha 214 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 209312_x_at 215 CCNA2 Cyclin A2 213226_at 216 HLA-DRA major histocompatibility complex, class II, DR 208894_at alpha 217 HLA-DPA1 major histocompatibility complex, class II, DP 211991_s_at alpha 1 218 HLA-DRB1 major histocompatibility complex, class II, DR beta 1 215193_x_at 219 HLA-DMA major histocompatibility complex, class II, DM 217478_s_at alpha 220 CCL19 chemokine (C-C motif) ligand 19 210072_at 221 HLA-E major histocompatibility complex, class I, E 200904_at 222 LST1 leukocyte specific transcript 1 211581_x_at 223 HLA-DQB1 major histocompatibility complex, class II, DQ 209823_x_at beta 1 224 CXCL3 chemokine (C—X—C motif) ligand 3 207850_at 225 HLA-DRB1 Major histocompatibility complex, class II, DR beta 3 208306_x_at 226 STAT5A signal transducer and activator of transcription 5A 203010_at 227 HLA-E major histocompatibility complex, class I, E 200905_x_at 228 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta 201288_at 229 CD1E CD1E antigen, e polypeptide 215784_at 230 CR2 complement component (3d/Epstein Barr virus) 205544_s_at receptor 2 231 IGH immunoglobulin heavy constant gamma 1 (G1m 211430_s_at marker) 232 HLA-E major histocompatibility complex, class I, E 217456_x_at 233 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 201137_s_at 234 HLA-G HLA-G histocompatibility antigen, class I, G 211529_x_at 235 IGJ Immunoglobulin J polypeptide 212592_at 236 CXCL1 chemokine (C—X—C motif) ligand 1 204470_at 237 CXCL12 chemokine (C—X—C motif) ligand 12 209687_at 238 HLA-DOB major histocompatibility complex, class II, DO 205671_s_at beta 239 GBP2 guanylate binding protein 2, interferon-inducible 202748_at 240 C3 complement component 3 217767_at 241 HLA-C major histocompatibility complex, class I, C 211799_x_at 242 IFITM3 interferon induced transmembrane protein 3 (1-8 U) 212203_x_at 243 CXCL12 chemokine (C—X—C motif) ligand 12 203666_at 244 AZGP1 alpha-2-glycoprotein 1, zinc 217014_s_at 245 HLA-B major histocompatibility complex, class I, B 211911_x_at 246 HLA-G HLA-G histocompatibility antigen, class I, G 210514_x_at 247 IL2RG interleukin 2 receptor, gamma 204116_at 248 CD74 CD74 antigen 209619_at 249 HLA-B major histocompatibility complex, class I, B 208729_x_at 250 MBP myelin basic protein 207323_s_at 251 HLA-DQA1 /// major histocompatibility complex, class II, DQ 212671_s_at HLA-DQA2 alpha 1 252 HLA-G HLA-G histocompatibility antigen, class I, G 211528_x_at 253 CHUK conserved helix-loop-helix ubiquitous kinase 209666_s_at 254 TNFRSF17 tumor necrosis factor receptor superfamily, 206641_at member 17 255 FCER1A Fc fragment of IgE, high affinity I, receptor for; 211734_s_at alpha polypeptide 256 HLA-F major histocompatibility complex, class I, F 204806_x_at 257 HLA-DRB4 major histocompatibility complex, class II, DR beta 4 215669_at 258 HFE hemochromatosis 206086_x_at 259 C7 complement component 7 202992_at 260 CXCL5 chemokine (C—X—C motif) ligand 5 214974_x_at 261 RPL3 ribosomal protein L3 211666_x_at 262 RPS9 ribosomal protein S9 217747_s_at 263 RPL5 ribosomal protein L5 200937_s_at 264 RPS6 ribosomal protein S6 200081_s_at 265 EIF4B eukaryotic translation initiation factor 4B 211938_at 266 RPS5 ribosomal protein S5 200024_at 267 EIF3S4 eukaryotic translation initiation factor 3, subunit 4 208887_at delta, 44 kDa 268 RPL35A ribosomal protein L35a 213687_s_at 269 RPL10A ribosomal protein L10a 200036_s_at 270 RPL29 ribosomal protein L29 200823_x_at 271 RPL22 ribosomal protein L22 220960_x_at 272 RPL4 ribosomal protein L4 211710_x_at 273 MTA1 metastasis associated 1 202247_s_at 274 EIF3S7 eukaryotic translation initiation factor 3, subunit 7 200005_at zeta, 66/67 kDa 275 RPL24 ribosomal protein L24 200013_at 276 RPL22 ribosomal protein L22 221726_at 277 RPS16 ribosomal protein S16 201258_at 278 EIF2C2 Eukaryotic translation initiation factor 2C, 2 213310_at 279 RPL14 ribosomal protein L14 200074_s_at 280 RPL18A ribosomal protein L18a 200869_at 281 MRPL24 mitochondrial ribosomal protein L24 218270_at 282 MRPL9 mitochondrial ribosomal protein L9 209609_s_at 283 RPS6 ribosomal protein S6 201254_x_at 284 RPL4 ribosomal protein L4 201154_x_at 285 RPL11 Ribosomal protein L11 200010_at 286 PABPC4 poly(A) binding protein, cytoplasmic 4 (inducible 201064_s_at form) 287 RPL18 ribosomal protein L18 200022_at 288 KIAA0256 KIAA0256 gene product 212450_at 289 RPS19 ribosomal protein S19 213414_s_at 290 RPS2 Ribosomal protein S2 221798_x_at 291 EIF4B eukaryotic translation initiation factor 4B 211937_at 292 EIF3S1 eukaryotic translation initiation factor 3, subunit 1 208264_s_at alpha, 35 kDa 293 RPL21 ribosomal protein L21 200012_x_at 294 RPS8 ribosomal protein S8 200858_s_at 295 RPS6 ribosomal protein S6 209134_s_at 296 RPL39 ribosomal protein L39 208695_s_at 297 ORC6L origin recognition complex, subunit 6 homolog-like 219105_x_at 298 RRM2 ribonucleotide reductase M2 polypeptide 201890_at 299 Pfs2 DNA replication complex GINS protein PSF2 221521_s_at 300 RRM2 ribonucleotide reductase M2 polypeptide 209773_s_at 301 NFIB Nuclear factor I/B 213033_s_at 302 FEN1 flap structure-specific endonuclease 1 204767_s_at 303 RFC3 replication factor C (activator 1) 3, 38 kDa 204127_at 304 NAP1L1 nucleosome assembly protein 1-like 1 208752_x_at 305 TCL1B T-cell leukemia/lymphoma 1B 206413_s_at 306 PIAS3 protein inhibitor of activated STAT, 3 203035_s_at 307 BIRC5 baculoviral IAP repeat-containing 5 (survivin) 202095_s_at 308 JTB jumping translocation breakpoint 210434_x_at 309 WHSC1 Wolf-Hirschhorn syndrome candidate 1 209054_s_at 310 JTB jumping translocation breakpoint 200048_s_at 311 PTTG1 pituitary tumor-transforming 1 203554_x_at 312 ABCB6 ATP-binding cassette, sub-family B (MDR/TAP), 203192_at member 6 313 GPR56 G protein-coupled receptor 56 212070_at 314 HDHD3 haloacid dehalogenase-like hydrolase domain 221256_s_at containing 3 315 PDHX pyruvate dehydrogenase complex, component X 203067_at 316 ATP9A ATPase, Class II, type 9A 212062_at 317 LPGAT1 lysophosphatidylglycerol acyltransferase 1 202651_at 318 PSAT1 phosphoserine aminotransferase 1 220892_s_at 319 GALNS galactosamine (N-acetyl)-6-sulfate sulfatase 206335_at 320 GFPT1 glutamine-fructose-6-phosphate transaminase 1 202722_s_at 321 ACACB acetyl-Coenzyme A carboxylase beta 221928_at 322 FLJ21963 FLJ21963 protein 219616_at 323 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6- 202464_s_at biphosphatase 3 324 SCLY selenocysteine lyase 59705_at 325 RDH11 retinol dehydrogenase 11 217776_at 326 PECI peroxisomal D3,D2-enoyl-CoA isomerase 218025_s_at 327 ATP2C1 ATPase, Ca++ transporting, type 2C, member 1 209935_at 328 GSTP1 glutathione S-transferase pi 200824_at 329 INSIG1 insulin induced gene 1 201626_at 330 SH2D1A SH2 domain protein 1A, Duncan's disease 210116_at 331 CCR2 chemokine (C-C motif) receptor 2 206978_at 332 — — 211567_at 333 GNLY granulysin 205495_s_at 334 RALA v-ral simian leukemia viral oncogene homolog A 214435_x_at (ras related) 335 CCR7 chemokine (C-C motif) receptor 7 206337_at 336 SOCS5 suppressor of cytokine signaling 5 209648_x_at 337 SOCS5 suppressor of cytokine signaling 5 208127_s_at 338 NDN necdin homolog (mouse) 209550_at 339 IGFBP7 insulin-like growth factor binding protein 7 201162_at 340 MAC30 hypothetical protein MAC30 212279_at 341 SOCS1 suppressor of cytokine signaling 1 213337_s_at 342 IGFBP7 insulin-like growth factor binding protein 7 213910_at 343 MORF4L1 mortality factor 4 like 1 217982_s_at 344 HTRA1 HtrA serine peptidase 1 201185_at 345 CTGF connective tissue growth factor 209101_at 346 NEDD9 neural precursor cell expressed, developmentally 202149_at down-regulated 9 347 IGFBP7 insulin-like growth factor binding protein 7 201163_s_at 348 ESM1 endothelial cell-specific molecule 1 208394_x_at 349 OGFR opioid growth factor receptor 211513_s_at 350 OGFR opioid growth factor receptor 211512_s_at 351 RGS4 regulator of G-protein signalling 4 204337_at 352 RGS16 regulator of G-protein signalling 16 209324_s_at 353 RGS3 regulator of G-protein signalling 3 220300_at 354 RGS2 regulator of G-protein signalling 2, 24 kDa 202388_at 355 GRK5 G protein-coupled receptor kinase 5 204396_s_at 356 COL2A1 collagen, type II, alpha 1 217404_s_at 357 SHOX2 short stature homeobox 2 210135_s_at 358 COL10A1 collagen, type X, alpha 1 205941_s_at 359 AEBP1 AE binding protein 1 201792_at 360 MATN3 matrilin 3 206091_at 361 SHOX2 short stature homeobox 2 208443_x_at 362 TWIST1 twist homolog 1(Drosophila) 213943_at 363 ANKH ankylosis, progressive homolog (mouse) 220076_at 364 ANXA2 annexin A2 210427_x_at 365 POSTN periostin, osteoblast specific factor 210809_s_at 366 FGFR1 fibroblast growth factor receptor 1 210973_s_at 367 ANXA2 annexin A2 213503_x_at 368 CDC42BPA CDC42 binding protein kinase alpha (DMPK-like) 213595_s_at 369 MAPKAPK2 mitogen-activated protein kinase-activated protein 215050_x_at kinase 2 370 PAK2 p21 (CDKN1A)-activated kinase 2 208875_s_at 371 TAF1 TAF1 RNA polymerase II, TATA box binding 216711_s_at protein (TBP)-associated factor 372 PDGFRA platelet-derived growth factor receptor, alpha 203131_at polypeptide 373 CLK1 CDC-like kinase 1 214683_s_at 374 ADRBK1 adrenergic, beta, receptor kinase 1 201401_s_at 375 MAP4K5 mitogen-activated protein kinase kinase kinase 203552_at kinase 5 376 PRKD1 protein kinase D1 205880_at 377 PRKAR1A protein kinase, cAMP-dependent, regulatory, type 200604_s_at I, alpha 378 PCTK1 PCTAIRE protein kinase 1 207239_s_at 379 PTK9 PTK9 protein tyrosine kinase 9 214007_s_at 380 NEK7 NIMA (never in mitosis gene a)-related kinase 7 212530_at 381 PIK3R4 phosphoinositide-3-kinase, regulatory subunit 4, 212740_at p150 382 CDC42BPA CDC42 binding protein kinase alpha (DMPK-like) 215296_at 383 MAPKAPK2 mitogen-activated protein kinase-activated protein 201461_s_at kinase 2 384 MAP2K3 mitogen-activated protein kinase kinase 3 207667_s_at 385 PRPF4B PRP4 pre-mRNA processing factor 4 homolog B 202127_at (yeast) 386 BMP2K BMP2 inducible kinase 59644_at 387 PRKACG protein kinase, cAMP-dependent, catalytic, 207228_at gamma 388 MAP2K2 mitogen-activated protein kinase kinase 2 213490_s_at 389 MET met proto-oncogene (hepatocyte growth factor 211599_x_at receptor) 390 CASK calcium/calmodulin-dependent serine protein 211208_s_at kinase (MAGUK family) 391 ROR2 receptor tyrosine kinase-like orphan receptor 2 205578_at 392 MAPK10 mitogen-activated protein kinase 10 204813_at 393 PCTK1 PCTAIRE protein kinase 1 208824_x_at 394 RND3 Rho family GTPase 3 212724_at 395 PLEKHC1 pleckstrin homology domain containing, family C 209210_s_at member 1 396 SPOCK sparc/osteonectin, cwcv and kazal-like domains 202363_at proteoglycan (testican) 397 TGFB1I1 transforming growth factor beta 1 induced 209651_at transcript 1 398 LAMB1 laminin, beta 1 201505_at 399 LAMC1 laminin, gamma 1 (formerly LAMB2) 200771_at 400 ADAM12 ADAM metallopeptidase domain 12 (meltrin 213790_at alpha) 401 THBS2 thrombospondin 2 203083_at 402 HNT neurotrimin 222020_s_at 403 CDH6 cadherin 6, type 2, K-cadherin (fetal kidney) 205532_s_at 404 MLLT4 myeloid/lymphoid or mixed-lineage leukemia; 215904_at translocated to, 4 405 CLSTN1 calsyntenin 1 201561_s_at 406 CDH5 cadherin 5, type 2, VE-cadherin (vascular 204677_at epithelium) 407 PLEKHC1 pleckstrin homology domain containing, family C 214212_x_at (with FERM domain) member 1 408 PPFIBP1 PTPRF interacting protein, binding protein 1 (liprin 214375_at beta 1) 409 SRPX sushi-repeat-containing protein, X-linked 204955_at 410 PKP3 plakophilin 3 209873_s_at 411 ITGB3BP integrin beta 3 binding protein (beta3-endonexin) 205176_s_at 412 ADRM1 adhesion regulating molecule 1 201281_at 413 NCAM1 neural cell adhesion molecule 1 212843_at 414 PCDH17 protocadherin 17 205656_at 415 COL6A3 collagen, type VI, alpha 3 201438_at 416 PLXNC1 plexin C1 213241_at 417 COL5A3 collagen, type V, alpha 3 218975_at 418 SLC2A3 solute carrier family 2, member 3 202499_s_at 419 FUT3 fucosyltransferase 3 216010_x_at 420 SLC3A1 solute carrier family 3, member 1 205799_s_at 421 HEXA hexosaminidase A (alpha polypeptide) 201765_s_at 422 SFRS11 splicing factor, arginine/serine-rich 11 200686_s_at 423 CDC40 cell division cycle 40 homolog (yeast) 203376_at 424 PRPF4 PRP4 pre-mRNA processing factor 4 homolog 209162_s_at (yeast) 425 SFRS9 splicing factor, arginine/serine-rich 9 201698_s_at 426 SFRS11 splicing factor, arginine/serine-rich 11 200685_at 427 PRPF18 PRP18 pre-mRNA processing factor 18 homolog 221546_at (yeast) 428 DHX15 DEAH (Asp-Glu-Ala-His) box polypeptide 15 201385_at 429 THOC1 THO complex 1 204064_at 430 SFPQ Splicing factor proline/glutamine-rich 214016_s_at 431 LSM8 LSM8 homolog, U6 small nuclear RNA associated 219119_at 432 EDNRA endothelin receptor type A 204464_s_at 433 ELK3 ELK3, ETS-domain protein (SRF accessory 221773_at protein 2) 434 IDE insulin-degrading enzyme 203328_x_at 435 PRKAB1 protein kinase, AMP-activated, beta 1 non- 201835_s_at catalytic subunit 436 IDE insulin-degrading enzyme 217496_s_at 437 PTPN11 protein tyrosine phosphatase, non-receptor type 209895_at 11 438 PTPN1 protein tyrosine phosphatase, non-receptor type 1 202716_at 439 ARFRP1 ADP-ribosylation factor related protein 1 215984_s_at 440 CYTL1 cytokine-like 1 219837_s_at 441 GNRH1 gonadotropin-releasing hormone 1 207987_s_at 442 GNG11 guanine nucleotide binding protein (G protein), 204115_at gamma 11 443 CDC42SE1 CDC42 small effector 1 218157_x_at 444 PDE4B phosphodiesterase 4B, cAMP-specific 211302_s_at 445 IPO8 importin 8 205701_at 446 IQGAP1 IQ motif containing GTPase activating protein 1 213446_s_at 447 CASP8AP2 CASP8 associated protein 2 222201_s_at 448 GTF2I general transcription factor II, I 201065_s_at 449 CD40 CD40 antigen (TNF receptor superfamily member 35150_at 5) 450 GNG12 guanine nucleotide binding protein (G protein), 212294_at gamma 12 451 MARCKSL1 MARCKS-like 1 200644_at 452 CHRNA3 cholinergic receptor, nicotinic, alpha polypeptide 3 210221_at 453 KIR2DL4 killer cell immunoglobulin-like receptor, two 211245_x_at domains, long cytoplasmic tail, 4 454 KIR2DL4 killer cell immunoglobulin-like receptor, two 211242_x_at domains, long cytoplasmic tail, 4 455 OR3A2 olfactory receptor, family 3, subfamily A, member 2 221386_at 456 TXNIP thioredoxin interacting protein 201008_s_at 457 COPS2 COP9 constitutive photomorphogenic homolog 202467_s_at subunit 2 (Arabidopsis) 458 EPOR erythropoietin receptor 396_f_at 459 KHDRBS1 KH domain containing, RNA binding, signal 201488_x_at transduction associated 1 460 WDR68 WD repeat domain 68 221745_at 461 NR2F1 Nuclear receptor subfamily 2, group F, member 1 209505_at 462 — — 213401_s_at 463 ARL2BP ADP-ribosylation factor-like 2 binding protein 202091_at 464 TXNIP thioredoxin interacting protein 201009_s_at 465 MPP2 membrane protein, palmitoylated 2 (MAGUK p55 213270_at subfamily member 2) 466 MCC mutated in colorectal cancers 206132_at 467 MAPK9 mitogen-activated protein kinase 9 203218_at 468 PAK4 p21(CDKN1A)-activated kinase 4 33814_at 469 SMAD2 SMAD, mothers against DPP homolog 2 203077_s_at (Drosophila) 470 DPYSL3 dihydropyrimidinase-like 3 201431_s_at 471 TLR4 toll-like receptor 4 221060_s_at 472 WIF1 WNT inhibitory factor 1 204712_at 473 LGALS3BP lectin, galactoside-binding, soluble, 3 binding 200923_at protein 474 APPL adaptor protein containing pH domain, PTB 218158_s_at domain and leucine zipper motif 1 475 DRD5 dopamine receptor D5 208486_at 476 TRPC1 transient receptor potential cation channel, 205802_at subfamily C, member 1 477 PKD2 polycystic kidney disease 2 (autosomal dominant) 203688_at 478 TRPC1 transient receptor potential cation channel, 205803_s_at subfamily C, member 1 479 ATP13A3 ATPase type 13A3 212297_at 480 TRPA1 transient receptor potential cation channel, 208349_at subfamily A, member 1 481 SLC24A3 solute carrier family 24 219090_at (sodium/potassium/calcium exchanger), member 3 482 RNF19 ring finger protein 19 220483_s_at 483 LIPT1 lipoyltransferase 1 205571_at 484 RPN2 ribophorin II 208689_s_at 485 RABGGTB Rab geranylgeranyltransferase, beta subunit 213704_at 486 PDLIM2 PDZ and LIM domain 2 (mystique) 219165_at 487 DLG3 discs, large homolog 3 (neuroendocrine-dlg, 212729_at Drosophila) 488 TNS1 tensin 1 221748_s_at 489 SHANK2 SH3 and multiple ankyrin repeat domains 2 215829_at 490 CIT citron (rho-interacting, serine/threonine kinase 21) 212801_at 491 CRK v-crk sarcoma virus CT10 oncogene homolog 202226_s_at (avian) 492 RIN2 Ras and Rab interactor 2 209684_at 493 DLG3 discs, large homolog 3 (neuroendocrine-dlg, 207732_s_at Drosophila) 494 PDLIM7 PDZ and LIM domain 7 (enigma) 203370_s_at 495 SNX3 sorting nexin 3 213545_x_at 496 SNX3 sorting nexin 3 210648_x_at 497 SNX2 sorting nexin 2 202114_at 498 SNX24 sorting nexing 24 218705_s_at 499 NCF4 neutrophil cytosolic factor 4, 40 kDa 205147_x_at 500 PSEN1 presenilin 1 207782_s_at 501 SNX3 sorting nexin 3 200067_x_at 502 PIK3R2 phosphoinositide-3-kinase, regulatory subunit 2 207105_s_at (p85 beta) 503 STAT2 signal transducer and activator of transcription 2, 205170_at 113 kDa 504 TRAF3IP2 TRAF3 interacting protein 2 215411_s_at 505 RIN3 Ras and Rab interactor 3 219457_s_at 506 PARD3 par-3 partitioning defective 3 homolog (C. elegans) 221526_x_at 507 TAX1BP3 Tax1 binding protein 3 209154_at 508 TRAF3IP2 TRAF3 interacting protein 2 202987_at 509 HNRPA1 heterogeneous nuclear ribonucleoprotein A1 222040_at 510 HNRPR heterogeneous nuclear ribonucleoprotein R 208765_s_at 511 — — 221919_at 512 SIP1 survival of motor neuron protein interacting protein 1 205063_at 513 SRRM1 serine/arginine repetitive matrix 1 201224_s_at 514 IVNS1ABP influenza virus NS1A binding protein 201362_at 515 DNM3 dynamin 3 209839_at 516 FLJ14107 hypothetical protein FLJ14107 207287_at 517 ZFPM2 zinc finger protein, multitype 2 219778_at 518 FOXO1A forkhead box O1A 202724_s_at 519 SMARCA2 SWI/SNF related, matrix associated, actin 212257_s_at dependent regulator of chromatin, subfamily a, member 2 520 NFYC nuclear transcription factor Y, gamma 202216_x_at 521 CRSP9 cofactor required for Sp1 transcriptional activation, 204349_at subunit 9, 33 kDa 522 HOXC6 homeo box C6 206858_s_at 523 TCF4 Transcription factor 4 213891_s_at 524 SMARCC1 SWI/SNF related, matrix associated, actin 201073_s_at dependent regulator of chromatin, subfamily c, member 1 525 SMARCA5 SWI/SNF related, matrix associated, actin 213251_at dependent regulator of chromatin, subfamily a, member 5 526 ID4 Inhibitor of DNA binding 4, dominant negative 209292_at helix-loop-helix protein 527 FOS v-fos FBJ murine osteosarcoma viral oncogene 209189_at homolog 528 ZNF161 zinc finger protein 161 202172_at 529 PDGFB platelet-derived growth factor beta polypeptide 216061_x_at 530 MTCP1 mature T-cell proliferation 1 205106_at 531 HYPE Huntingtin interacting protein E 219910_at 532 E2F4 E2F transcription factor 4, p107/p130-binding 38707_r_at 533 PPM1D protein phosphatase 1D magnesium-dependent, 204566_at delta isoform 534 CCND3 cyclin D3 201700_at 535 MAPRE1 microtubule-associated protein, RP/EB family, 200712_s_at member 1 536 SPHAR S-phase response (cyclin-related) 206272_at 537 PICALM phosphatidylinositol binding clathrin assembly 212511_at protein 538 DARS aspartyl-tRNA synthetase 201624_at 539 VAMP4 vesicle-associated membrane protein 4 213480_at 540 TAPBP TAP binding protein (tapasin) 208829_at 541 RANBP9 RAN binding protein 9 216125_s_at 542 DAG1 dystroglycan 1 (dystrophin-associated 212128_s_at glycoprotein 1) 543 EPRS glutamyl-prolyl-tRNA synthetase 200841_s_at 544 RPL26L1 ribosomal protein L26-like 1 218830_at 545 RPL34 ribosomal protein L34 200026_at 546 RPL31 ribosomal protein L31 200963_x_at 547 MRPS18A mitochondrial ribosomal protein S18A 221693_s_at 548 RPL36 ribosomal protein L36 219762_s_at 549 RPL31 ribosomal protein L31 221593_s_at 550 RPS25 ribosomal protein S25 200091_s_at 551 EIF3S2 eukaryotic translation initiation factor 3, subunit 2 208756_at beta, 36 kDa 552 MRPL33 mitochondrial ribosomal protein L33 203781_at 553 NAG neuroblastoma-amplified protein 202926_at 554 RPL24 ribosomal protein L24 214143_x_at 555 RCC1 regulator of chromosome condensation 1 215747_s_at 556 CUL5 cullin 5 203531_at 557 RBBP4 retinoblastoma binding protein 4 217301_x_at 558 ATR ataxia telangiectasia and Rad3 related 209903_s_at 559 PARD6A par-6 partitioning defective 6 homolog alpha 205245_at (C. elegans) 560 38967 septin 7 213151_s_at 561 RBL2 retinoblastoma-like 2 (p130) 212332_at 562 NOLC1 nucleolar and coiled-body phosphoprotein 1 205895_s_at 563 CCNT1 cyclin T1 206967_at 564 NM_006845 mitotic centromere-associated kinesin mitotic 209408 centromere-associated kinesin

Additional sequences SEQ ID NO: 501 tctttcccccttttaatttgtgatgtcacttgaccccatttatgtgtagg agcactacaccattggtttccaatactgcacacataagatacatacttgt gtgcagaaagtatcttcctccaggcttgtaatacccttcacatggaagat taatgagggaaatctttatattctgtataaaaacaaaagcaaatttatat actaaaatcatttgtctaaaaatttaagttgttttcaaataaaaattaaa atgcatttctgatatgcaaaaaaaaaaaaaaaaaaaaaaaaaaannnnnn nnnnannanngannanntaagtcacttgttgagagggattatttactaat tatatacttctcattcctgtaactccattccctttaaacagtggtgatat caaatatacttccatccattgaatggggtatttttaacaacaacaaaagt gatatactaaaaaatgtattgcttaaggcttattgaatcattttgaagca ctttgtgtatttgaaaactgctttataatctcattta SEQ ID NO: 502 tctctccatgttgggggtcctaactcccccaccccatatctacgtgtcct ccgggcattgccctctccatggctctggtcaccctgaccctctgccctgc ccaccgcaggtcccccggggtcccggaagccccttctggctgcacctgcc atgtttacagagggcccctgggctgcgcggccccagcctgggcaccctga tttttaagccatagacctggggtcagggcaggaaggaacttcactctgct gcttccgagaacctcggccgtgacattcggggccgggcgggacccgcccc acagactccaacttcccctccaaaccccgaagtgaaacccgccaccgggt taccccacaagggggccgctgcgagaagttcacccacccccgaaaaaata attaaactcgcaggccaggcacg SEQ ID NO: 503 tcccttccaagctgtgttaactgttcaaactcaggcctgtgtgactccat tggggtgagaggtgaaagcataacatgggtacagaggggacaacaatgaa tcagaacagatgctgagccataggtctaaataggatcctggaggctgcct gctgtgctgggaggtataggggtcctgggggcaggccagggcagttgaca ggtacttggagggctcagggcagtggcttctttccagtatggaaggattt caacattttaatagttggttaggctaaactggtgcatactggcattggcc ttggtggggagcacagacacaggataggactccatttctttcttccattc cttcatgtctaggataacttgctttcttctttcctttactcctggctcaa gccctgaatttcttcttttcctgcaggggttgagagctttctgccttagc ctaccatgtgaaactctaccctgaag SEQ ID NO: 504 cagaacactcatgtctacagctggcccaagaataaaaaaaacatcctgct gcggctgctgagagaggaagagtatgtggctcctccacgggggcctctng cccacccttncaggtggttcccttgtgacaccgttcatccccagatcact gaggccaggccatgtttggggccttgttctgacagcattctggctgaggc tggtcggtagcactcctggctggtttttttctgttcctccccgagaggcc ctctggcccccaggaaacctgttgtgcagagctcttccccggagacctcc acacaccctggctttgaagtggagtctgtgactgctctgcattctctgct tttaaaaaaaccattgcaggtgccagtgtcccatatgttccnnctgacag tttgatgtgnccattctgggcctctcagtgcttagcnagtagataatngt angggatgtggcagcaaatggnaatgactacaaacactctnctatcaatc acttcaggctacttttatgagttagccagatgcttgtgtatcctcagacc aaactg SEQ ID NO: 505 gaaagccttttgtccaaatatggaacttgaatgatatggcaaaattagaa atgcaattttagaagtaattacactgttgtgtaaatggccacctcttttg aagtctttgctacattgcttataaaacactgagttgaacatgagaaagcc ttttgtctgcagctgtacttttcaactggacatgaaccatgtacttttat ggcacgtagatattcacatcaaatttctgatttgcagaccgattttattt ttagttaacaaataagcnttatcnaaatgtggcttttgaactaaagcgct tttaattaaggagttataacagcatgttattttgagtagctgttactaaa atctgttgtgatggaacaatttggagtgagcatctgatatcagagataaa gagagaagcatgcagtgagcatctggaagttcttgtaaaaaaaaaaacaa attaaacattctcatttgaatgcatttaaaatttttttaaattgccaatt cctaagctttttctttgttagttg SEQ ID NO: 506 atcagtgattcagccgactgctctttgagtccagatgttgatccagttct tgcttttcaacgagaaggatttggacgtcagagtatgtcagaaaaacgca caaagcaattttcagatgccagtcaattggatttcgttaaaacacgaaaa tcaaaaagcatggatttaggtatagctgacgagactaaactcaatacagt ggatgaccagaaagcaggttctcccagcagagatgtgggtccttccctgg gtctgaagaagtcaagctcnttggagagtctgcagaccgcagttgccgag gtgactttgaatggggatattcctttccatcgtccacggccgcggataat cagaggcaggggatgcaatgagagcttcagagctgccatcgacaaatctt atgataaacccgcggtagatgatgatgatgaaggcatggagaccttggaa gaagacacagaagaaagttcaagatcagggagagagtctgtatccacagc cagtgatcagccttcccactctctggagagacaa SEQ ID NO: 507 atgtttttatcgtactctttggagatgcccattctacttttgaatttagc ttttactaattcgcatctggaagctcagcaagtgcacaagccttactttg gttaccgtg SEQ ID NO: 508 gtaagactttctgacatgtaacattagttccgtagttttgagacctggta gaactgactttcatatttggataacctggaaaacacccaaacacaaactt caagtcttctttctcttttttcattatcttttttagtctgaggtgacacc atcattaaggattcgacacccgtttgtaaataaaatgacatcagcaatta ctctgaaatgtttctagtttgcaaagatttagcaatgtgatgttattaac ccttcctcccttcagagacctgtcctaagctctgaaccactcattccttc cactcttcttaccccaggtggttgatgagcagtggtccctggtgt SEQ ID NO: 509 cagcaaaagaatgccctgcgttcccaaagtaaaagaatgacaagctgtac cttaaaccaaaacacttcgtaatctcatccaattgcaaaaagagttatta gccaaccaggtattcccagtagtgacagtggatataactgtgtagtcatt cacctctgcttatatgaatactttacaacctcttttgcct SEQ ID NO: 510 tggatatggctaccctccagattactacggctatgaagattactatgatg attactatggttatgattatcacgactatcgtggaggctatgaagatccc tactacggctatgatgatggctatgcagtaagaggaagaggaggaggaag gggagggcgaggtgctccaccaccaccaagggggaggggagcaccacctc caagaggtagagctggctattcacagaggggggcacctttgggaccacca agaggctctaggggtggcagagggggtcctgctcaacagcagagaggccg tggttcccgtggatctcggggcaatcgtgggggcaatgtaggaggcaaga gaaaggcagatgggtacaaccagcctgattccaagcgtcgtcagaccaac aaccaacagaactggggttcccaacccatcgctcagcagccgcttcagca aggtggtgactattctggtaac SEQ ID NO: 511 gaacagattttacttacatccatatagttacttaaagtccagttttctgt taaacatttttcttaatatattgagccaaaactagtccagttaagctgaa cttggtttttctggagatgaattgttttaaattgacaccctattgatggc tcccagttgaaggaagtgagcacattatttgtactgtgaatataaatttt tgcccttttatttatcttcctttgacccatttccttaaaataatggctca aagtaatagacttccccaaatggtggggggatgggtgggttattaatggg aggtatggggggtttagcttgagatgggacttggtcttagagctagttct SEQ ID NO: 512 aacaatgccaattcaagtacagatttcaacacatcttcaacactatgtga agggttcacatcttaacctgtgcaattcagattgatactcagaatatggg ttgatttgaatatctgaaatatcaatggaaaatcccactcagtttttgat gaacagtttgaacagttttctgtaatcaagcagcttgcatagaaattgta tgatgaaattttacataggttcttggtgctg SEQ ID NO: 513 ctccccctcctaaacgaagagcatcaccatctccaccaccaaagcggcgg gtctcccattctccacctcccaaacaaagaagctccccagtcaccaagag acgttcaccttcattatcatccaagcataggaaagggtcttccccaagcc gctctacccgggaggcccgatcaccacaaccaaacaaacggcattcgccc tcaccacggcctcgagctcctcagacctcctcaagtcctccacccgttcg aagaggagcgtcgtcatcaccccaaagaaggcagtccccgtctccaagta ctaggcccattaggagagtctccaggactccggaacctaaaaagataaaa aaggctgcttccccaagcccacagtctgtaagaagggtctcatcctcccg atctgtctccgggtctcctgagccagcagctaaaaagcccccagcacctc catcccccgtccagtctcagtcaccgtctacaaactggtcaccagctgta ccggtc SEQ ID NO: 514 gcaggaaatccttgcaccatgggattaatatccaattgctgcttgtacac tcattcattactaaaagttttgagaaatttttttttccagtaatgagctt aagaaatttgtggaaaataactcacctggcatcttacatctgaaataagg aatgatataaggtttttttttctcacagaagatgaagcacacaggaacct aatgggccaactgggatgaggtgactattctgagatgactattcagtggc taacttgggttaggaagaaaataattaggtattttctccaaatgttcact ggtactctgccactttatttctctcatctgttacacaaagaaccaccagg aaagcaaatcagtttggttggtaactctgtaattcctaactatcactggt ttggttctggactaaaactacattgacagattgaatttgcctaatatgat gactgtttttaatatggatctgtatgtgttctattcagcccaagga SEQ ID NO: 515 gagacttctcacttctggttggaggtttcacatatggctcaactcaagtc attaatctctttttaatttttactcttgaattccttaaacttcgctcatt atgaaatgttttaaaattatgacaaaaattactctgtctaaccacttgcc ttgtctgctaccagtttgttaaaaattattccccccaaccagtaattcca ccagtactacttgatttgtgttatatttcctatgtacatgtacagccttt gttttgcttgcttgtctatttttactttcccttttttgggtcaaattttt cttttgctttgtttgaagaaggaatatacagaagtaaaatcttgtcttct ctgctgattctttaattaatatgagccggatactttccactgtcttcttg gcactttcaggatttcttaatgctgatatatggactcttagaatggaatt tttgaagaaaaatctcaaagcctgtatcgttct SEQ ID NO: 516 ggctgtcagatggccttgagcggcaccaagtagaaaacgcgctcccaccc ctgaccttctcctcagcttcattgtgagacctcaagttcctcagcttcca ggatgatcaacctagctgaaaacctgaagtccctcccggtacaagtccaa gcagtccccagccagggagaccaggtgttgtctgacatcccacacacatc ggcacacttgggggattgcaaaagggaggaagggagccaaaggctagggc cccggggttcagctaacactcagcacccctcccaaagagcgccccctgtg tgttctggatctctagaggggtttggtttgggccaagtagtgcttagttt taattttctctttctggaaataaatacttttaataagtaaagatgctgct cagctgtcatatcctgcaaggttagaggaaagatgtgggccgtgcgcg SEQ ID NO: 517 atacacatgctataagttcgccttaagatttcaattcttggataatcagg ctctgtttgcactttatattttagcagatacagtctcttagtcactaggc tttgcatttgtatgtagctgtatgtttccgtccattttcttaatcctgaa cctgtatgttaaatgaagatggcaatttttttcttgtatagtacttgtat tttctttcgctgatgcagctctgtctcaatttttaaacctttgctgttaa atgcaatactttataaagaatgaacaaaattactggaagcagtattgtaa gtaatgaggtagtattaatcagttttatcttttgaaaggcacagtctaaa tcgaaaccctaaactcaatgctgcaagtatgaatttaattcatatataag atctatttaaatataagagtagcaatactgcacctggtgatca SEQ ID NO: 518 gagcagtaaatcaatggaacatcccaagaagaggataaggatgcttaaaa tggaaatcattctccaacgatatacaaattggacttgttcaactgctgga tatatgctaccaataaccccagccccaacttaaaattcttacattcaagc tcctaagagttcttaatttataactaattttaaaagagaagtttcttttc tggttttagtttgggaataatcattcattaaaaaaaatgtattgtggttt atgcgaacagaccaacctggcattacagttggcctctccttgaggtgggc acagcctggcagtgtggccaggggtggccatgtaagtcccatcaggacgt agtcatgcctcctgcatttcgctacccgagtttagtaacagtgcagattc cacgttcttgttccgatactctgagaagtgcctgatgttgatgtacttac agacacaagaacaatctttgctataa SEQ ID NO: 519 gcaaccacccatatatgtttcagcacattgaggaatcctttgctgaacac ctaggctattcaaatggggtcatcaatggggctgaactgtatcgggcctc agggaagtttgagctgcttgatcgtattctgccaaaattgagagcgacta atcaccgagtgctgcttttctgccagatgacatctctcatgaccatcatg gaggattattttgcttttcggaacttcctttacctacgccttgatggcac caccaagtctgaagatcgtgctgctttgctgaagaaattcaatgaacctg gatcccagtatttcattttcttgctgagcacaagagctggtggcctgggc ttaaatcttcaggcagctgatacagtggtcatctttgacagcgactgg SEQ ID NO: 520 gatcccggtgcagctgaatgccggccagctgcagtatatccgcttagccc agcctgtatcaggcactcaagttgtgcagggacagatccagacacttgcc accaatgctcaacagattacacagacagaggtccagcaaggacagcagca gttcagccagttcacagatggacagcagctctaccagatccagcaagtca ccatgcctgcgggccaggacctcgcccagcccatgttcatccagtcagcc aaccagccctccgacgggcaggccccccaggtgaccggcgactgagggcc tgagctggcaaggccaaggacacccaacacaatttttgccatacagcccc aggcaatgggcacagccttcctccccagaggacccggccgacctcagcgc ctcctgcaggctaggacactggtgcactacacc SEQ ID NO: 521 ttttccttttgataatagcatcatatattagttcattttcttttggacag tcttaagagaagtttcactaaaaatgtaaacagctttaatcttgactcca aatttttcaattatgagatgtcataggcagtaatttcgctgtataacaag catagacaaatgagtgtccctgcactaagaagaatcactttaaaaagcaa agtgttagctgctgttgtatgggacattcctatgttttagagttgcagta aaactttgatgataacctcaataatagcaaagtgg SEQ ID NO: 522 ggaccctgaactcagactctacagattgccctccaagtgaggacttggct cccccactccttcgacgcccccacccccgccccccgtgcagagagccggc tcctgggcctgctggggcctctgctccagggcctcagggccggcctggca gccggggagggccggagcggagggcgcgccttggccccacaccaaccccc agggcctccccgcagtccctgcctagcccctctgccccagcaaatgccca gcccaggcaaattgtatttaaagaatcctgggggtcattatggcatttta caaactgtgaccgtttctgtgtgaagatttttagctgtatttgtggtctc tgtatttatatttatgtttagcaccgtcagtgttcctatccaatttcaaa aaag SEQ ID NO: 523 gaaactgtatgggtagcttttttgtttgttttttgttttgtttttgtttt tgtttttgtttttagttgtaggtcgcagcggggaaattttttgcgactgt acacatagctgcagcattaaaaacttaaaaaaattgttaaaaaaanaaaa aaagggaaaacatttcaaaaaaaaaaaaanngataaacagttacaccttg ttttcaatgtgtggctgagtgcctcgattttttcatgtttttggtgtatt tctgatttgtagaagtgtccaaacaggttgtgtgctggagttccttcaag acaaaaacaaacccagcttggtcaaggccattacctgtttcccatctgta gttattcg SEQ ID NO: 524 cgcccaccaccatgagctggagtggggatgacaagacttgtgttcctcaa ctttcttgggtttctttcaggatttttcttctcacagctccaagcacgtg tcccgtgcctccccactcctcttaccacccctctctctgacactttttgt gttgggtcctcagccaacactcaaggggaaacctgtagtgacagtgtgcc ctggtcatccttaaaataacctgcatctcccctgtcctggtgtgggagta agctgacagtttctctgcaggtcctgtcaactttagcatgctatgtcttt accatttttgctctcttgcagttttttgctttgtcttatgcttctatgga taatgctatataatcattatctttttatctttctgttattattgttttaa aggagagcatcctaagttaataggaaccaaaaaataatgatgggcagaag ggggggaatagccacaggggacaaaccttaaggcattataagtgacctta tttctgcttttctgagctaagaatggtgctgatggtaaagtttgagactt ttgccacacacaa SEQ ID NO: 525 tttgtcatatgaccttctgaagcagccacaacttagataatgtcagaact aaggtganttttttttttttaattttgaaagcccagccaaaatgaggtgt gaatttgtcatactgttacattgaaattggtaacaaaatatatcccctcc catttggacttttagggtaaatgaaaattttattgtattttaaagtagtt tctaagtgttagcaagactgactataattccagtttctgttttctatgga cagacctgataaactggagaccctaaagcaggaatacccaaattatagtg tcaggattttagctgtaccagaggcctttatgtgctacacataatttgta taaaattttatatgtgcagattgggtacataaacagttctccatt SEQ ID NO: 526 gtgctacagatactacatttcaaagagttggcattttccctttggccact caagcagcatttgatgtatctaaagnaacaaagtcattgtttatttttta aaaaattatatgcagttgtacaagatactacattccattgaaatgttggc tatgtcctaaccaggcaaccagataacaaaaacattttgagtcttttatc taggtagttctaattattcagctacttagtttaacaaaggaaaatatcct gacttctctcatttcatttgtagacttttcattgtataggcacaaccaaa gagtcagactggtttaaaactccagaaggaaaaaaagtatcccacacagt ggatgttgtttctaagaatgctacaaaatcctgacatctcagacatctca atgttaaaggaagaaaaaaaataccttttcatttcaaagaactaatatac tttgatattgtgtaaaccttactcaagtttattgtcaagctttaactgcc tttttagaactttttaaaatttcgagcccacaaatctat SEQ ID NO: 527 ctgcccgagctggtgcattacagagaggagaaacacatcttccctagagg gttcctgtagacctagggaggaccttatctgtgcgtgaaacacaccaggc tgtgggcctcaaggacttgaaagcatccatgtgtggactcaagtccttac ctcttccggagatgtagcaaaacgcatggagtgtgtattgttcccagtga cacttcagagagctggtagttagtagcatgttgagccaggcctgggtctg tgtctcttttctctttctccttagtcttctcatagcattaactaatctat tgggttcattattggaattaacctggtgctggatattttcaaattgtatc tagtgcagctgattttaacaataactactgtgttcctggcaatagtgtgt tctg SEQ ID NO: 528 gagacttcattgtatgacttcagttaaaatactattttgtatgcattctt tattcacttaagaagcttgtctgcaataataaagccacgtcatgtcttct ttngggagggagagagtcgatggcaggagggggttttgggtgggccactg aaaaggggtaccgaataggttgtgtgatgaaattctgtgtcttggaactg gaattgagtttcgatgttgatgaactgattcaaccaggtgttgaaggcac gacagccactgctctacgaaaaggcagagtacgtttttcccttctggttg taacctggttgagagcttcccctttatcagattggcagctaaacagttgt attagataatccttaaatctgacatccagcctgttacgctctagggctcg ctgcttggcctgcgtttgctttttattgtgtatccgttcccctcctacgg tgtgctcctgaatgaaggtttctatgtaagcagatgatgattttacctgt caataccagcactgtattactaacatgca SEQ ID NO: 529 tgcccttccaggtgggtgtgggacacctgggagaaggtctccaagggagg gtgcagccctcttgcccgcacccctccctgcttgcacacttccccatctt tgatccttctgagctccacctctggtggctcctcctaggaaaccagctcg tgggctgggaatgggggagagaagggaaaagntccccaagaccccctggg gtgggatntgagctcccacctcccttnccacntantgcactttccccctt cccgccttccaaaacctgcttcdttcagtttgtaaagtcggtgattatat ttttgggggctttccttttattttttaaatgtaaaatttatttatattcc gtatttaaagttgtaaaaaaaaataaccacaaaacaaaaccaaaaaaaaa aaaaaacttctcctcctgcagccgggagcggccggcctgcctccctgcgc acccgcagcctcccccgctgcctccctagggctcccctccggccgccagc gcccatttttcattccctagatagag SEQ ID NO: 530 tgatgaatcccacaaaagtcagcaccttctacagaacagatgccctgatc accaaggacttggtactgatttagagagaagagagcagctcctagcagca tcaacatctatttgtcgcttatttgccctgc SEQ ID NO: 531 gaagccggcaggtttcggacaacacaggtcctggtcggacaccacatccc tccccatccgcaggatgtggaaaagcagatgcaggagtttgtacagtggc tcaactccgaggaagccatgaacctgcacccagtggagtttgcagcctta gcccattataaactcgtttacatccaccctttcattgatggcaacgggag gacctcccgtctgctcatgaacctcatcctcatgcaggcgggctacccgc ccatcaccatccgcaaggagcagcggtccgactactaccacgtgttggaa gctgccaacgagggcgacgtgaggcctttcattcgcttcatcgccaagtg tactgagaccaccctggacaccctgctttttgccacaactgagtactcgg tggcactgccagaagcccaacccaaccactctgggttcaaggagacgctt cctgtgaagcccta SEQ ID NO: 532 ccaaagtgtttgcttctccctttctgcggccttcgccagcccaggctcgg ctgccacccagtggnacagaaccgaggagctgccattnncccccatangg gnnagtgtcttgttncnnnnnnnnnnnnnnntcnttgcttctgncagctc cttcccctaggagggaagggtggggtggaactgggcacatgccagcacc SEQ ID NO: 533 gccacttgtcttgaaaactgtgcaactttttaaagtaaattattaagcag actggaaaagtgatgtattttcatagtgacctgtgtttcacttaatgttt cttagagccaagtgtcttttaaacattattttttatttctgatttcataa ttcagaactaaatttttcatagaagtgttgagccatgctacagttagtct tgtcccaattaaaatactatgcagtatctcttacatcagtagcatttttc taaaaccttagtcatcagatatgcttactaaatcttcagcatagaaggaa gtgtgtttgcctaaaacaatctaaaacaattcccttctttttcatcccag accaatggcattattaggtcttaaagtagttactcccttctcgtgtttgc ttaaaatatgtgaagttttccttgctatttcaataacagatggtgctgct aattcccaacatt SEQ ID NO: 534 ttgcatttggattggggtccctctaaaatttaatgcatgatagacacata tgagggggaatagtctagatggctcctctcagtactttggaggcccctat gtagtccgtgctgacagctgctcctagagggaggggcctaggcctcagcc agagaagctataaattcctctttgctttgctttctgctcagcttctcctg tgtgattgacagctttgctgctgaaggctcattttaatttattaattgct ttgagcacaactttaagaggacataatgggggcctggccatccacaagtg gtggtaaccctggtggttgctgttttcctcccttctgctactggcaaaag gatctttgtggccaaggagctgctatagcctggggtggggtcatgccctc ctctcccattgtccctctgccccatcctccagcagggaaaatgcagcagg gatgccctggaggtggctgagcccctgtctagagagggaggcaagccctg ttgacacaggtctttcctaaggctgcaaggtttaggctggtggccc SEQ ID NO: 535 gggggaaaacgaccctgtattgcagaggattgtagacattctgtatgcca cagatgaaggctttgtgatacctgatgaagggggcccacaggaggagcaa gaagagtattaacagcctggaccagcagagcaacatcggaattcttcact ccaaatcatgtgcttaactgtaaaatactcccttttgttatccttagagg actcactggtttcttttcataagcaaaaagtacctcttcttaaagtgcac tttgcagacgtttcactccttttccaataagtttgagttaggagctttta ccttgtagcagagcagtattaacanctagttggttcacctggaaaacaga gaggctgaccgtggggctcaccatgcggatgcgggtcacactgaatgctg gagagatgttatgtaatatgctgaggtggcgacctcagtggagaaatg SEQ ID NO: 536 agctttcttcaccttatatatgttcttccactgtgactttttagttgaag actagtaaattaacttttagttagaagatgcctactgcttttgttgttta ttttaatcagcagagcacagagacacataaaaactctgggaaatgactag gataaaaatatcagtatgtatctgttttagatattttgagttttgctttt tttatgccttgaatattttatttcaaaaagtatctgaagcaaattctcag actgaactacttcttagacctcactgtaagaatattttattcaatgtctc atttatgatagatttgcaagctgctcatttttgaacagctttttgcatgg gataggagcatgtctattctaacacatcagcttattcaaaagcaagaatt ttaaaaataagataaatgtaaagttgttttataaacgatcctgttaatta aaccacagacaccatatatccttctgca SEQ ID NO: 537 tacccaggtgattatatttgttgatctaataanatggaaggtttgtttta tatgaattttcaaaaagatgtctctttacactttttgttaccttgtagac tcttattgataaatgcaactacttattaaaattgttcacttttngtcttt tgatcagatgcctttagtcaggtaagtttaagggaaaatacgcagtttaa tgttttggtacatataattatgtctgccaaagaaacctttgattgtatca tattgcctatttagtagtgcatagggttcagagtacatgataaaggatca aaagctttgcattgataagtgtctcataatatttgctgtgatt SEQ ID NO: 538 cacttattcttttcagtaacctgctagtgcacaggctgtactttaggtac ttaaaatatgcactagaataaatttgcaaggccctaaaatatcactgtta tttttggagtaattcagtataggttcgtttaaaagagatttttataactt cagacatgcatcagtaggaaataacttgagaaattcatatggttatgtta caaattcatattctgttactacagtaaacgttaagagttttaaacagtta agattgtacaatttttcttcttttctatattacaagggccccagtgttaa tgtcttagattttcagtatttgaacttatttttttaaattctgtcattga gataagaataattcaggtagcatctgaaattttaatgaatgtataattgg catatcatggaaaattaaccagaaagtatcagttcttaaaagttatgcct ag SEQ ID NO: 539 gaagccacaaagatgccacatgttagtatatcagtgagaggtgactccac agtgctctctggagaagcaatatgagtgactgaagagtggggccttttgc ttttgcctggatataggggtgctcttctactgtaattgggtgtggaaaaa ctctggctttatggtattccattaggttcttttcatttaaagtagtctta aaatcaaagtatccaatattttaaagccacaaagtagattacataattag cagagattttagtcagtaaaatgttagaaatcaaactataagaaaattca agtcctttattttgtgtcttgggtatatgtcattattttaaattccacac tcccttatttaatcactttggtaagtgcctttgatgttttgaaatgtata gtgggagatgagcaaatgtaaatgtcatgtgccctgttccctagcttctc aattcctcataaccatttttaccagtgttgcaaagtttagacctttgtgt taatatcagaagtgtatttgtagcccctccatagtgaacaatga SEQ ID NO: 540 ttcttcagccctagatggtgctcgccagacctcctctcaatgctcatcac acacagggctattcctttcctccaatgaaccaaaccgcctcccgcccacc tccaggtcccagtcctctgttccctttgcctggtccacccttgccctccc tgggtcgcagacgaggtcggcctcgtcattccccgcagaccgccgcgcgt ccctcttgtgcggttcaccacagttgtatttaagtgatcgtgtgagtcgt cgttaaatgcctgtctccccgcggatcatgggctcctcgaggacagggac tggcctgtctgtccactgctgtaaccccgcgccggcatagggacctaagg cccactggagggcgctcatcaagtagctgctggatgttgacgaaggaagc ggcggcgcagctcagggatctccgagtcaggacggtcggcc SEQ ID NO: 541 aacaatacctgcttttacaccaagaatggacatagtttaggtattgcttt cactgacctaccgccaaatttgtatcctgttagtcctcgaccttttagta gtccaagtatgagccccagccatggaatgaatatccacaatttagcatca ggcaaaggaagcaccgcacatttttcaggttttgaaagttgtagtaatgg tgtaatatcaaataaagcacatcaatcatattgccatagtaataaacacc agtcatccaactttcaatgtaccagaactaaacagtataaatatgtcaag atcacagcaagttaataacttcaccagtaatgatgtagacatggaaatag atcactactccaatggagttggagaaacttcatccaatggtttcctaaat ggtagctctaaacatgaccacgaaatggaagattgtgacaccgaaatgga agttgattcaagtcagttgagacgtcagttgtgtggaggaagtcaggccg ccatagaaagaatgatccactttggacgagagctgcaa SEQ ID NO: 542 cacttccagcccatgtacactagtggcccacgaccaaggggtcttcattt ccatgaaaaagggactccaagaggcagtggtggctgtggcccccaacttt ggtgctccagggtgggccagctgcttgtgggggcacctgggaggtcaaag gtctccaccacatcaacctattttgttttaccctttttctgtgcattgtt tttttttttcctcctaaaaggaatatcacggttttttgaaacactcagtg ggggacattttggtgaagatgcaatatttttatgtcatgtgatgctcttt cctcacttgaccttggccgctttgtcctaacagtccacagtcctgccccg acccaccccatcccttttctctggcactccagtcccaggccttgggcctg aactactggaaaaggtctggcggctggggaggagtgccagcaa SEQ ID NO: 543 acttcgctacttggctagagttgcaactacagctgggttatatggctcta atctgatggaacatactgagattgatcactggttggagttcagtgctaca aaattatcttcatgtgattcctttacttctacaattaatgaactcaatca ttgcctgtctctgagaacatacttagttggaaactccttgagtttagcag atttatgtgtttgggccaccctaaaaggaaatgctgcctggcaagaacag ttgaaacagaagaaagctccagttcatgtaaaacgttggtttggctttct tgaagcccagcaggccttccagtcagtaggtaccaagtgggatgtttcaa caaccaaagctcgagtggcacctgagaaaaagcaagatgttgggaaattt gttgagcttccaggtgcggagatgggaaaggttaccgtcagatttcctcc agaggccagtggttacttacacattgggcatgcaaaagctgctcttctga accagcactaccaggt SEQ ID NO: 544 ccctcacacgtgcgcaggaagatcatgtcatccccgctctccaaggagct gcggcagaagtacaatgtccgctccatgcccatccgcaaggacgacgagg tccaggtagttcgaggacactacaaaggtcagcaaattggcaaggtagtc caggtgtacagaaagaaatatgtcatctacatcgagcgggtgcagcgtga gaaggccaacggcacaactgtccacgtgggcattcacccaagcaaggtgg ttatcaccaggctaaaactggacaaggatcggaaaaaaattcttgaacgc aaagccaagtctcgacaagttggaaaagagaaaggcaaatataaagaaga acttattgagaaaatgcaggaataaatagaacctgttgtgcaaccacggt ttaaccggagattttgaggctagggtgtgtttctttcgaacttttcggaa tgtctggaacatttcatttcctgttttgttacctgtgcctctgtaaatct SEQ ID NO: 545 tgcaggcactcagaatggtccagcgtttgacataccgacgtaggctttcc tacaatacagcctctaacaaaactaggctgtcccgaacccctggtaatag aattgtttacctttataccaagaaggttgggaaagcaccaaaatctgcat gtggtgtgtgcccaggcaaacttcgaggggttcgtcctgtaagacctaaa gttcttatgagattgtccaaaacaaagaaacatgtcagcagggcctatgg tggttccatgtgtgctaaatgtgttcgtgacaggatcaagcgtgctttcc tta SEQ ID NO: 546 cgcagaatggctcccgcaaagaagggtggcgagaagaaaaagggccgttc tgccatcaacgaagtggtaacccgagaatacaccatcaacattcacaagc gcatccatggagtgggcttcaagaagcgtgcacctcgggcactcaaagag attcggaaatttgccatgaaggagatgggaactccagatgtgcgcattga caccaggctcaacaaagctgtctgggccaaaggaataaggaatgtgccat accgaatccgtgtgcggctgtccagaaaacgtaatgaggatgaagattca ccaaataagctatatactttggttacctatgtacctgttaccactt SEQ ID NO: 547 tgttctgctgcttagccagttcatccggcctcatggaggcatgctgcccc gaaagatcacaggcctatgccaggaagaacaccgcaagatcgaggagtgt gtgaagatggcccaccgagcaggtctattaccaaatcacaggcctcggct tcctgaaggagttgttccgaagagcaaaccccaactcaaccggtacctga cgcgctgggctcctggctccgtcaagcccatctacaaaaaaggcccccgc tggaacagggtgcgcatgcccgtggggtcaccccttctgagggacaatgt ctgctactcaagaacaccttggaagctgtatcactgacagagagcagtgc ttccagagttcctcctgcacctgtgctggggagtaggaggcccactcaca agcccttggccacaactatactcctgtcccaccccaccacgatggcctgg tccctccaacatgcatggacaggggacagtgggactaacttcagtaccct tggcctgcacagtagcaatgc SEQ ID NO: 548 cctatggccgtgggcctcaacaagggccacaaagtgaccaagaacgtgag caagcccaggcacagccgacaccgcgggcgtctgaccaaacacaccaagt tcgtgcgggacatgattcgggaggtgtgtggctttgccccgtacgagcgg cgcgccatggagttactgaaggtctccaaggacaaacgggccctcaaatt tatcaagaaaagggtggggacgcacatccgc SEQ ID NO: 549 tcaaaagtaagttctccatcccataaagccatttaaattcattagaaaaa tgtccttacctcttaaaatgtgaattcatctgttaagctaggggtgacac acgtcattgtaccctttttaaattgttggtgtgggaagatgctaaagaat gcaaaactgatccatatctgggatgtaaaaaggttgtggaaaatagaatg tccagacccgtctacaaaaggtttttagagttgaaatatgaaatgtgatg tgggtatggaaattgactgttacttcctttacagatctacagacagt SEQ ID NO: 550 gccgcctaaggacgacaagaagaagaaggacgctggaaagtcggccaaga aagacaaagacccagtgaacaaatccgggggcaaggccaaaaagaagaag tggtccaaaggcaaagttcgggacaagctcaataacttagtcttgtttga caaagctacctatgataaactctgtaaggaagttcccaactataaactta taaccccagctgtggtctctgagagactgaagattcgaggctccctggcc agggcagcccttcaggagctccttagtaaaggacttatcaaactggtttc aaagcacagagctcaagtaatttacaccagaaataccaagggtggagatg ctccagctgctggtgaagatgcatgaataggtccaaccagctgta SEQ ID NO: 551 cccccaactatgaccatgtggtcctgggcggtggtcaggaagccatggat gtaaccacaacctccaccaggattggcaagtttgaggccaggttcttcca tttggcctttgaagaagagtttggaagagtcaagggtcactttggaccta tcaacagtgttgccttccatcctgatggcaagagctacagcagcggcggc gaagatggttacgtccgtatccattacttcgacccacagtacttcgaatt tga SEQ ID NO: 552 ggtgagcgaagctgggacaggtttctgcttcaacaccaagagaaaccgac tgcgggaaaaactgactcttttgcattatgatccagttgtgaaacaaaga gtcctcttcgtggaaaagaaaaaaatacgctccctttaaacggtggattg aaaatgactttgatttataaagagaagactgagggcggggatactgattc agaaatcctgtagcgtgtaataaaagaagaggaaatggcatggaatcact gcctcctgtgatttgaaggccattgtgaaggaaaacaatgcagtgaaaga aagttcttcatattaggacagatatcattgcatcacatttatttatcttt SEQ ID NO: 553 gtcgctctttgtataacaccaagcagatgctgcctgcagagggtgtgaag gagctgtgtctgctgctgcttaaccagtccctcctgcttccatctctgaa acttctcctcgagagccgagatgagcatctgcacgagatggcactggagc aaatcacggcagtcactacggtgaatgattccaattgtgaccaagaactt ctttccctgctcctggatgccaagctgctggtgaagtgtgtctccactcc cttctatccacgtattgttgaccacctcttggctagcctccagcaagggc gctgggatgcagaggagctgggcagacacctgcgggaggccggccatgaa gccgaagccgggtctctccttctggccgtgagggggactcaccaggcctt cagaaccttcagtacagccctccgcgcagcacagcactgggtgttgaagc cacctgtggccctgctccttagcagaaaaagcatctggagttgaatgctg ttcccagaagcaacatgtgtatctgccgattgttctccatggttccaaca a SEQ ID NO: 554 ggctaagcaagcatctaaaaagactgcaatggctgctgctaaggcaccta caaaggcagcacctaagcnaaagattgtgaagcctgtgaaagtttcagct ccccgagttggtggaaaacgctaaactggcagatta SEQ ID NO: 555 cccagaacctaacatccttcaagaattccaccaagtcctgggtgggcttc tctggtggccagcaccatacagtctgcatggattcggaaggaaaagcata cagcctgggccgggctgagtatgggcggctgggccttggagagggtgctg aggagaagagcatacccaccctcatctccaggctgcctgctgtctcctcg gtggcttgtggggcctctgtggggtatgctgtgaccaaggatggtcgtgt tttcgcctggggcatgggcaccaactaccagctgggcacagggcaggatg aggacgcctggagccctgtggagatgatgggcaaacagctggagaaccgt gtggtcttatctgtgtccagcgggggccagcatacagtcttattagtcaa ggacaaagaacagagctgatgaagcctctgagggcctggcttctgtcctg cacaacctccctcacagaacagggaagcagtgacagctgcagatggcagc gggcctct SEQ ID NO: 556 gtaagatgtctctagcactgctcaaagggcaaattttaaaacttcagtct gggtgaaagatttgctagttttacagaaagatttgctatcttaaactcaa gctggtttttctgttctcatgtaagtgactgggatgctgtcttatgaatt cttccaaggtcatgtttgtgaaataaacattacatgagagctttcctgtc atctacactatatgttgtctggagtgttgaacaaatttattttagtttct aagttgtaatctatcctcatatggtctatacgattttgaatgtgtgccac tacatactgagatgataatgctgtacaattttaagtggtagcagtttctg tatgcagta SEQ ID NO: 557 aagccactcagttgatgctcacactgctgaagtgaactgcctttctttca atccttatagtgagttcattcttgccacaggatcagctgacaagactgtt gccttgtgggatctgagaaatctgaaacttaagttgcattcctttgagtc acataaggatgaaatattccaggttcagtggtcacctcacaatgagacta ttttagcttccagtggtactgatcgcagactgaatgtctgggatttaagt aaaattggagaggaacaatccccagaagatgcagaagacgggccaccaga gttgttgtttattcatggtggtcatactgccaagatatctgatttctcct ggaatcccaatgaaccttgggtgatttgttctgtatcagaagacaatatc atgcaagtgtggcaaatggagttagtccttgaccactagtttgatgccat ctccattttgggtgacctgtttcaccagcaggc SEQ ID NO: 558 aggccaagacccatgttcttgacattgagcagcgactacaaggtgtaatc aagactcgaaatagagtgacaggactgccgttatctattgaaggacatgt gcattaccttatacaggaagctactgatgaaaacttactatgccagatgt atcttggttggactccatatatgtgaaatgaaattatgtaaaagaatatg ttaataatctaaaagtaatgcatttggtatgaatctgtggttgtatctgt tcaattctaaagtacaacataaatttacgttctcagcaactgttatttct ctctg SEQ ID NO: 559 gtacgtgggggtctggctgagagtacagggctgctggcggtcagtgatga gatcctcgaggtcaatggcattgaagtagccgggaagaccttggaccaag tgacggacatgatggttgccaacagccataacctcattgtcactgtcaag cccgccaaccagcgcaataacgtggtgcgaggggcatctgggcgtttgac aggtcctccctctgcagggcctgggcctgctgagcctgatagtgacgatg acagcagtgacctggtcattgagaaccgccagcctcccagttccaatggg ctgtctcaggggcccccgtgctgggacctgcaccctggctgccgacatcc tggtacccgcagctctctgccctccctggatgaccaggagcaggccagtt ctggctgggggagtcgcattcgaggagatggtagtggcttcagcctctga cagtcaggatgaagccccatgccactccacactgctgggacatggcaggg acttcacagtgggggtttttagctggctcaca SEQ ID NO: 560 atatgcttactgtgcacctagagcttttttataacaacgtctttttgttt gtttgnttttggattctttaaatatatattattctcatttagtgccctct ttagccagaatctcattactgcttcatttttgtaataacatttaatttag atattttccatatattggcactgctaaaatagaatatagcatctttcata tggtaggaaccaacaaggaaactttcctttaactccctttttacacttta tggtaagtagcagggggggaaatgcatttatagatcatttctaggcaaaa ttgtgaagctaatgaccaacctgtttctacctatatgcagtctctttatt ttactagaaatgggaatcatggcctcttgaagagaaaaaagtcaccattc tgcatttagctgtattcatat SEQ ID NO: 561 gcacaagctgtgacaggctccatccagcccctcagtgctcaggccctggc tggaagtctgagctctcaacaggtgacaggaacaactttgcaagtccctg gtcaagtggccattcaacagatttccccaggtggccaacagcagaagcaa ggccagtctgtaaccagcagtagtaatagacccaggaagaccagctcttt atcgcttttctttagaaaggtataccatttagcagctgtccgccttcggg atctctgtgccaaactagatatttcagatgaantgaggaaaaaaatctgg acctgctttgaattctccataattcagtgtcctgaacttatgatggacag acatctggaccagttattaatgtgtgccatttatgtgatggcaaaggtca caaaagaagataagtccttccagaacattatgcgttgttataggactcag ccgcaggcccggagccaggtgtataga SEQ ID NO: 562 catcatccccattccgaagggtcagggaggaggaaattgaggtggattca cgagttgcggacaactcctttgatgccaagcgaggtgcagccggagactg gggagagcgagccaatcaggttttgaagttcaccaaaggcaagtcctttc ggcatgagaaaaccaagaagaagcggggcagctaccggggaggctcaatc tctgtccaggtcaattctattaagtttgacagcgagtgacctgaggccat cttcggtgaagcaagggtgatgatcggagactacttactttctccagtgg acctgggaaccctcaggtctctaggtgagggtcttgatgaggacagaagt ttagagtaggtcctaagactttacagtgtaacatcctctctggtcc SEQ ID NO: 563 gtttgatcatccagccaagattgccaagagtactaaatcctcttccctaa atttctccttcccttcacttcctacaatgggtcagatgcctgggcatagc tcagacacaagtggcctttccttttcacagcccagctgtaaaactcgtgt ccctcattcgaaactggataaagggcccactggggccaatggtcacaaca cgacccagacaatagactatcaagacactgtgaatatgcttcactccctg ctcagtgcccagggtgttcagcccactcagcccactgcatttgaatttgt tcgtccttatagtgactatctgaatcctcggtctggtggaatctcctcga ga SEQ ID NO: 564 atctgtttggtttgacacccagcctcttccctggccctccccagagaact ttgggtacctggtgggtctaggcagggtctgagctgggacaggttctggt aaatgccaagtatgggggcatctgggcccagggcagctggggagggggtc agagtgacatgggacactccttttctgttcctcagttgtcgccctcacga gaggaaggagctcttagttacccttttgtgttgcccttctttccatcaag gggaatgttctcagcatagagctttctccgcagcatcctgcctgcgtgga ctggctgctaatggagagctccctggggttgtcctggctctggggagaga gacggagcctttagtacagctatctgctggctctaaaccttctacgcctt tgggccgagcactgaatgtcttgtact 

1. A method for predicting distant metastasis of lymph node negative primary breast cancer comprising the steps of: a) obtaining breast cancer cells; b) isolating nucleic acid and/or protein from the cells; and c) analyzing the nucleic acid and/or protein to determine the presence, expression level or status of a Biomarker selected from the pathways in Table
 4. 2. The method according to claim 1 wherein gene expression is analyzed by determining the expression of the biomarkers corresponding to those listed in Table 1, Table 5 or Table
 6. 3. A composition comprising an oligonucleotide related to the markers listed in Table 1, Table 5 or Table
 6. 4. A kit comprising biomarker detection agents for performing the method according to claim
 1. 5. An article comprising biomarker detection agents for performing the method according to claim
 1. 